Methods and apparatus for analyzing polynucleotide sequences

ABSTRACT

Methods for high speed, high throughput analysis of polynucleotide sequences, and apparatuses with which to carry out the methods are provided in the invention.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application claims benefit of Ser. No. 60/163,742 filed Nov. 4,1999; and is a CIP of Ser. No. 09/605,520 filed Jun. 27, 2000; whichclaims benefit of Ser. No. 60/141,503 filed Jun. 28, 1999; and claimsbenefit of Ser. No. 60/147,199 filed Aug. 3, 1999; and claims benefit ofSer. No. 60/186,856 filed Mar. 3, 2000.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSOREDRESEARCH AND DEVELOPMENT

Work described herein has been supported, in part, by NIH grantsHG-01642-02. The U. S. Government may therefore have certain rights inthe invention.

TECHNICAL FIELD

The present invention relates to methods for high speed, high throughputanalysis of polynucleotide sequences and apparatuses for carrying outsuch methods.

BACKGROUND OF THE INVENTION

Traditional DNA sequencing techniques share three essential steps intheir approaches to sequence determination. First, a multiplicity of DNAfragments are generated from a DNA species which it is intended tosequence. These fragments are incomplete copies of the DNA species to besequenced. The aim is to produce a ladder of DNA fragments, each asingle base longer than the previous one. For example, with the Sangermethod (Sanger et al., Proc. Natl. Acad. Sci. USA 74:5463, 1977), thetarget DNA is used as a template for a DNA polymerase to produce anumber of incomplete clones. These fragments, which differ in respectivelength by a single base, are then separated on an apparatus which iscapable of resolving single-base differences in size. The third andfinal step is the determination of the nature of the base at the end ofeach fragment. When ordered by the size of the fragments which theyterminate, these bases represent the sequence of the original DNAspecies.

Automated systems for DNA sequence analysis have been developed, such asdiscussed in Toneguzzo et al., 6 Biotechniques 460, 1988; Kanbara etal., 6 Biotechnology 816, 1988; and Smith et al., 13 Nuc. Acid. Res. 13:2399, 1985; U.S. Pat. No. 4,707,237 (1987). However, all these methodsstill require separation of DNA products by a gel permeation procedureand then detection of their locations relative to one another along theaxis of permeation or movement through the gel. These apparatuses usedin these methods are not truly automatic sequencers. They are merelyautomatic gel readers, which require the standard sequencing reactionsto be carried out before samples are loaded onto the gel.

The disadvantages of the above methods are numerous. The most seriousproblems are caused by the requirement for the DNA fragments to besize-separated on a polyacrylamide gel. This process is time-consuming,uses large quantities of expensive chemicals, and severely limits thenumber of bases which can be sequenced in any single experiment, due tothe limited resolution of the gel. Sanger dideoxy sequencing has a readlength of approximately 500 bp, a throughput that is limited by gelelectrophoresis (appropriately 0.2%).

Other methods for analyzing polynucleotide sequences have been developedmore recently. In some of these methods broadly termed sequencing bysynthesis, template sequences are determined by priming the templatefollowed by a series of single base primer extension reactions (e.g., asdescribed in WO 93/21340, WO 96/27025, and WO 98/44152). While the basicscheme in these methods no longer require separation of polynucleotideson the gel, they encounter various other problems such as consumption oflarge amounts of expensive reagents, difficulty in removing reagentsafter each step, misincorporation due to long exchange times, the needto remove labels from the incorporated nucleotide, and difficulty todetect further incorporation if the label is not removed. Many of thesedifficulties stem directly from limitations of the macroscopic fluidicsemployed. However, small-volume fluidics have not been available. As aresult, these methods have not replaced the traditional gel-basedsequencing schemes in practice. The skilled artisans are to a largeextent still relying on the gel-based sequencing methods.

Thus, there is a need in the art for methods and apparatuses for highspeed and high throughput analysis of longer polynucleotide sequenceswhich can be automated utilizing the available scanning and detectiontechnology. The present invention fulfills this and other needs.

SUMMARY OF THE INVENTION

In one aspect of the present invention, methods for analyzing thesequence of a target polynucleotide are provided. The methods includethe steps of (a) providing a primed target polynucleotide linked to amicrofabricated synthesis channel; (b) flowing a first nucleotidethrough the synthesis channel under conditions whereby the firstnucleotide attaches to the primer, if a complementary nucleotide ispresent to serve as template in the target polynucleotide; (c)determining presence or absence of a signal, the presence of a signalindicating that the first nucleotide was incorporated into the primer,and hence the identity of the complementary base that served as atemplate in the target polynucleotide; (d) removing or reducing thesignal, if present; and (e) repeating steps (b)-(d) with a furthernucleotide that is the same or different from the first nucleotide,whereby the further nucleotide attaches to the primer or a nucleotidepreviously incorporated into the primer.

In some methods, step (a) comprises providing a plurality of differentprimed target polynucleotides linked to different synthesis channels;step (b) comprises flowing the first nucleotide through each of thesynthesis channels; and step (c) comprises determining presence orabsence of a signal in each of the channels, the presence of a signal ina synthesis channel indicating the first nucleotide was incorporatedinto the primer in the synthesis channel, and hence the identity of thecomplementary base that served as a template in the targetpolynucleotide in the synthesis channel. In some methods, a plurality ofdifferent primed target polynucleotides are linked to each synthesischannels.

Some methods include the further steps of flushing the synthesis channelto remove unincorporated nucleotides. In some methods, steps (b)-(d) areperformed at least four times with four different types of nucleotides.In some methods, steps (b)-(d) are performed until the identity of eachbase in the target polynucleotide has been identified.

In some methods, the nucleotides are labeled. The label can be afluorescent dye, and the signal can be detected optically. The label canalso be a radiolabel, and the signal can be detected with aradioactivity detector. In some methods, incorporation of nucleotides isdetected by measuring pyrophosphate release.

In some methods, the synthesis channel is formed by bonding amicrofluidic chip to a flat substrate. In some of these methods, thetarget polynucleotides are immobilized to the interior surface of thesubstrate in the synthesis channel. In some of these methods, theinterior surface is coated with a polyelectrolyte multilayer (PEM). Insome of these methods, the microfluidic chip is fabricated with anelastomeric material such as RTV silicone.

In another aspect of the present invention, methods for analyzing atarget polynucleotide entails (a) pretreating the surface of a substrateto create surface chemistry that facilitates polynucleotide attachmentand sequence analysis; (b) providing a primed target polynucleotideattached to the surface; (c) providing a labeled first nucleotides tothe attached target polynucleotide under conditions whereby the labeledfirst nucleotide attaches to the primer, if a complementary nucleotideis present to serve as template in the target polynucleotide; (d)determining presence or absence of a signal from the primer, thepresence of a signal indicating that the labeled first nucleotide wasincorporated into the primer, and hence the identity of thecomplementary base that served as a template in the targetpolynucleotide; and (e) repeating steps (c)-(d) with a labeled furthernucleotide that is the same or different from the first labelednucleotide, whereby the labeled further nucleotide attaches to theprimer or a nucleotide previously incorporated into the primer.

In some of these methods, the substrate is glass and the surface iscoated with a polyelectrolyte multilayer (PEM). In some methods, the PEMis terminated with a polyanion. In some methods, the polyanion isterminated with carboxylic acid groups. In some methods, the targetpolynucleotide is biotinylated, and the PEM-coated surface is furthercoated with biotin and then streptavidin.

In still another aspect of the present invention, methods of analyzing atarget polynucleotide are provided which include the steps of (a)providing a primed target polynucleotide; (b) providing a first type ofnucleotide of which a fraction is labeled under conditions whereby thefirst nucleotide attaches to the primer, if a complementary nucleotideis present to serve as template in the target polynucleotide; (c)determining presence or absence of a signal from the primer, thepresence of a signal indicating the first nucleotide was incorporatedinto the primer, and hence the identity of the complementary base thatserved as a template in the target polynucleotide; and (d) repeatingsteps (b)-(c) with a further type of nucleotide of which a fraction islabeled the same and which is the same or different from the first typeof nucleotide, whereby the further nucleotide attaches to the primer ora nucleotide previously incorporated into the primer.

In some of these methods, the label used is a fluorescent label. In someof these methods, the removing or reducing step is performed byphotobleaching. In some of these methods, the fraction of labelednucleotides are less than 10%, less than 1%, less than 0.1%, or lessthan 0.01%.

In another aspect of the present invention, apparatuses for analyzingthe sequence of a polynucleotide are provided. The apparatuses have (a)a flow cell with at least one microfabricated synthesis channel; and (b)an inlet port and an outlet port which are in fluid communication withthe flow cell and which flowing fluids such as deoxynucleosidetriphosphates and nucleotide polymerase into and through the flow cell.Some of the apparatuses additionally have (c) a light source to directlight at a surface of the synthesis channel; and (d) a detector todetect a signal from the surface.

In some of the apparatuses, the synthesis channel is formed by bonding amicrofluidic chip to a flat substrate. In some apparatuses, themicrofluidic chip also contain microfabricated valves andmicrofabricated pumps in an integrated system with the synthesischannel. In some of these apparatuses, a plurality of reservoirs forstoring reaction reagents are also present, and the microfabricatedvalve and pump are connected to the reservoirs. In some apparatuses, thedetector is a photon counting camera. In some of the apparatuses, the tomicrofluidic chip is fabricated with an elastomeric material such as RTVsilicone. The substrate of some of the apparatuses is a glass coverslip. The cross section of the synthesis channel in some of theapparatuses has a linear dimension of less than 100 μm×100 μm, less than10 μm×100 μm, less than 1 μm×10 μm, or less than 0.1 μm×1 μm.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is an illustration of a first elastomeric layer formed on top ofa micromachined mold.

FIG. 2 is an illustration of a second elastomeric layer formed on top ofa micromachined mold.

FIG. 3 is an illustration of the elastomeric layer of FIG. 2 removedfrom the micromachined mold and positioned over the top of theelastomeric layer of FIG. 1

FIG. 4 is an illustration corresponding to FIG. 3, but showing thesecond elastomeric layer positioned on top of the first elastomericlayer.

FIG. 5 is an illustration corresponding to FIG. 4, but showing the firstand second elastomeric layers bonded together.

FIG. 6 is an illustration corresponding to FIG. 5, but showing the firstmicromachine mold removed and a planar substrate positioned in itsplace.

FIG. 7A is an illustration corresponding to FIG. 6, but showing theelastomeric structure sealed onto the planar substrate.

FIGS. 7B is a front sectional view corresponding to FIG. 7A, showing anopen flow channel.

FIG. 7C corresponds to FIG. 7A, but shows a first flow channel closed bypressurization in second flow channel.

FIG. 8 is an illustration of a first elastomeric layer deposited on aplanar substrate.

FIG. 9 is an illustration showing a first sacrificial layer deposited ontop of the first elastomeric layer of FIG. 8.

FIG. 10 is an illustration showing the system of FIG. 9, but with aportion of the first sacrificial layer removed, leaving only a firstline of sacrificial layer.

FIG. 11 is an illustration showing a second elastomeric layer applied ontop of the first elastomeric layer over the first line of sacrificiallayer of FIG. 10, thereby encasing the sacrificial layer between thefirst and second elastomeric layers.

FIG. 12 corresponds to FIG. 11, but shows the integrated monolithicstructure produced after the first and second elastomer layers have beenbonded together.

FIG. 13 is an illustration showing a second sacrificial layer depositedon top of the integral elastomeric structure of FIG. 12.

FIG. 14 is an illustration showing the system of FIG. 13, but with aportion of the second sacrificial layer removed, leaving only a secondline of sacrificial layer.

FIG. 15 is an illustration showing a third elastomer layer applied ontop of the second elastomeric layer and over the second line ofsacrificial layer of FIG. 14, thereby encapsulating the second line ofsacrificial layer between the elastomeric structure of FIG. 12 and thethird elastomeric layer.

FIG. 16 corresponds to FIG. 15, but shows the third elastomeric layercured so as to be bonded to the monolithic structure composed of thepreviously bonded first and second elastomer layers.

FIG. 17 corresponds to FIG. 16, but shows the first and second lines ofsacrificial layer removed so as to provide two perpendicularoverlapping, but not intersecting, flow channels passing through theintegrated elastomeric structure.

FIG. 18 is an illustration showing the system of FIG. 17, but with theplanar substrate thereunder removed.

FIG. 19 illustrates valve opening vs. applied pressure for various flowchannels.

FIG. 20 illustrates time response of a 100 μm×100 μm×10 μm RTVmicrovalve.

FIG. 21 is a schematic illustration of a multiplexed system adapted topermit flow through various channels.

FIG. 22A is a plan view of a flow layer of an addressable reactionchamber structure.

FIG. 22B is a bottom plan view of a control channel layer of anaddressable reaction chamber structure.

FIG. 22C is an exploded perspective view of the addressable reactionchamber structure formed by bonding the control channel layer of FIG.22B to the top of the flow layer of FIG. 22A.

FIG. 22D is a sectional elevation view corresponding to FIG. 22C, takenalong line 28D—28D in FIG. 22C.

FIG. 23 is a schematic of a system adapted to selectively direct fluidflow into any of an array of reaction wells.

FIG. 24 is a schematic of a system adapted for selectable lateral flowbetween parallel flow channels.

FIG. 25 is a schematic of an integrated system for analyzingpolynucleotide sequences.

FIG. 26 is a schematic of a further integrated system for analyzingpolynucleotide sequences.

FIG. 27 is a schematic diagram of a sequencing apparatus.

DETAILED DESCRIPTION I. Overview

The present invention provides methods and apparatuses for analyzingpolynucleotide sequences.

In some methods, the sequencing apparatuses comprise a microfabricatedflow channel to which polynucleotide templates are attached. Optionally,the apparatuses comprise a plurality of microfabricated channels, anddiverse polynucleotide templates can be attached to each channel. Theapparatuses can also have a plurality of reservoirs for storing variousreaction reagents, and pumps and valves for controlling flow of thereagents. The flow cell can also have a window to allow opticalinterrogation.

In these methods, single stranded polynucleotide templates with primersare immobilized to the surface of the microfabricated channel or to thesurface of reaction chambers that are disposed along a microfabricatedflow channel, e.g., with streptavidin-biotin links. After immobilizationof the templates, a polymerase and one of the four nucleotidetriphosphates are flowed into the flow cell, incubated with thetemplate, and flowed out. If no signal is detected, the process isrepeated with a different type of nucleotide.

These methods are advantageous over the other sequencing by synthesismethods discussed previously. First, use of microfabricated sequencingapparatuses reduces reagent consumption. It also increases reagentexchange rate and the speed of sequence analysis. In addition, themicrofabricated apparatuses provides parallelization: many synthesischannels can be built on the same substrate. This allows analysis of aplurality of diverse polynucleotide sequences simultaneously. Further,due to the reduction of time and dead volume for exchanging reagentsbetween different steps during the analysis, mismatch incorporation isgreatly reduced. Moreover, the read length is also improved becausethere is less time for the polymerase to incorporate a wrong nucleotideand it is less likely that the polymerase falls off the template. Allthese advantages result in high speed and high throughput sequenceanalysis regimes.

In some methods of the present invention, the surface of a substrate(e.g., a glass cover slip) is pretreated to create optimal surfacechemistry that facilitates polynucleotide template attachment andsubsequent sequence analysis. In some of these methods, the substratesurface is coated with a polyelectrolyte multilayer (PEM). Following thePEM coating, biotin can be applied to the PEM, and followed byapplication of streptavidin. The substrate surface can then be used toattach biotinylated-templates. The PEM-coated substrate providessubstantial advantages for immobilizing the template polynucleotides andfor polymerase extension reaction. First, because PEM can easily beterminated with polymers bearing carboxylic acids, it is easy to attachpolynucleotides. Second, the attached template is active for extensionby polymerases—most probably, the repulsion of like charges prevents thetemplate from “laying down” on the surface. Finally, the negative chargerepels nucleotides, and nonspecific binding is low.

In some other methods of the present invention, only a small percentageof each type of nucleotides present in the extension reaction islabeled, e.g., with fluorescent dye. As a result, relatively smallnumbers of incorporated nucleotides are fluorescently labeled,interference of energy transfer is minimized, and the polymerase is lesslikely to fall off the template or be “choked” by incorporation of twolabeled nucleotides sequentially. Optionally, the incorporatedfluorescent signals are extinguished by photobleaching. Employment ofphotobleaching strategy can reduce the number of steps (e.g., it may notbe necessary to perform the removal of label after every extensioncycle). These advantages lead to more accurate detection of incorporatedsignals, more efficient consumption of polymerase, and a fast sequencingmethod.

II. Definitions

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by those of ordinary skillin the art to which this invention pertains. The following referencesprovide one of skill with a general definition of many of the terms usedin this invention: Singleton et al., DICTIONARY OF MICROBIOLOGY ANDMOLECULAR BIOLOGY (2d ed. 1994); THE CAMBRIDGE DICTIONARY OF SCIENCE ANDTECHNOLOGY (Walker ed., 1988); and Hale & Marham, THE HARPER COLLINSDICTIONARY OF BIOLOGY (1991). Although any methods and materials similaror equivalent to those described herein can be used in the practice ortesting of the present invention, the preferred methods and materialsare described. The following definitions are provided to assist thereader in the practice of the invention.

The terms “nucleic acid” or “nucleic acid molecule” refer to adeoxyribonucleotide or ribonucleotide polymer in either single- ordouble-stranded form, and unless otherwise limited, can encompass knownanalogs of natural nucleotides that can function in a similar manner asnaturally occurring nucleotides.

“Nucleoside” includes natural nucleosides, including ribonucleosides and2′-deoxyribonucleosides, as well as nucleoside analogs having modifiedbases or sugar backbones.

A “base” or “base-type” refers to a particular type of nucleosidic base,such as adenine, cytosine, guanine, thymine, uracil, 5-methylcytosine,5-bromouracil, 2-aminopurine, deoxyinosine, N⁴-methoxydeoxycytosine, andthe like.

“Oligonucleotide” or “polynucleotide” refers to a molecule comprised ofa plurality of deoxyribonucleotides or nucleoside subunits. The linkagebetween the nucleoside subunits can be provided by phosphates,phosphonates, phosphoramidates, phosphorothioates, or the like, or bynonphosphate groups as are known in the art, such as peptoid-typelinkages utilized in peptide nucleic acids (PNAs). The linking groupscan be chiral or achiral. The oligonucleotides or polynucleotides canrange in length from 2 nucleoside subunits to hundreds or thousands ofnucleoside subunits. While oligonucleotides are preferably 5 to 100subunits in length, and more preferably, 5 to 60 subunits in length, thelength of polynucleotides can be much greater (e.g., up to 100 kb).

Specific hybridization refers to the binding, duplexing, or hybridizingof a molecule only to a particular nucleotide sequence under stringentconditions. Stringent conditions are conditions under which a probe canhybridize to its target subsequence, but to no other sequences.Stringent conditions are sequence-dependent and are different indifferent circumstances. Longer sequences hybridize specifically athigher temperatures. Generally, stringent conditions are selected to beabout 5° C. lower than the thermal melting point (T_(m)) for thespecific sequence at a defined ionic strength and pH. The T_(m) is thetemperature (under defined ionic strength, pH, and nucleic acidconcentration) at which 50% of the probes complementary to the targetsequence hybridize to the target sequence at equilibrium. Typically,stringent conditions include a salt concentration of at least about 0.01to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and thetemperature is at least about 30° C. for short probes (e.g., 10 to 50nucleotides). Stringent conditions can also be achieved with theaddition of destabilizing agents such as formamide or tetraalkylammonium salts. For example, conditions of 5×SSPE (750 mM NaCl, 50 mM NaPhosphate, 5 mM EDTA, pH 7.4) and a temperature of 25-30° C. aresuitable for allele-specific probe hybridizations. (See Sambrook et al.,Molecular Cloning 1989).

By “analysis of polynucleotide sequence of a template” is meantdetermining a sequence of at least 3 contiguous base subunits in asample fragment, or alternatively, where sequence information isavailable for a single base-type, the relative positions of at least 3subunits of identical base-types occurring in sequential order in thefragment. An example of the latter meaning is a determined sequence“AXXAXA” (5′>3′), where a series of 3 adenine (A) bases are found to beseparated by two and then one other base-type in the sample fragment.

The term “primer” refers to an oligonucleotide, whether occurringnaturally as in a purified restriction digest or produced synthetically,which is capable of acting as a point of initiation of synthesis whenplaced under conditions in which synthesis of a primer extension productwhich is complementary to a nucleic acid strand is induced, (i.e., inthe presence of nucleotides and an inducing agent such as DNA polymeraseand at a suitable temperature and pH). The primer is preferably singlestranded for maximum efficiency in amplification, but can alternativelybe double stranded. If double stranded, the primer is first treated toseparate its strands before being used to prepare extension products.Preferably, the primer is an oligodeoxyribonucleotide. The primer mustbe sufficiently long to prime the synthesis of extension products in thepresence of the inducing agent. The exact lengths of the primers dependon many factors, including temperature, source of primer and the use ofthe method.

A primer is selected to be “substantially” complementary to a strand ofspecific sequence of the template. A primer must be sufficientlycomplementary to hybridize with a template strand for primer elongationto occur. A primer sequence need not reflect the exact sequence of thetemplate. For example, a non-complementary nucleotide fragment can beattached to the 5′ end of the primer, with the remainder of the primersequence being substantially complementary to the strand.Non-complementary bases or longer sequences can be interspersed into theprimer, provided that the primer sequence has sufficient complementaritywith the sequence of the template to hybridize and thereby form atemplate primer complex for synthesis of the extension product of theprimer.

The term “probe” refers to an oligonucleotide (i.e., a sequence ofnucleotides), whether occurring naturally as in a purified restrictiondigest or produced synthetically, recombinantly or by PCR amplification,which is capable of hybridizing to another oligonucleotide of interest.A probe can be single-stranded or double-stranded. Probes are useful inthe detection, identification and isolation of particular genesequences. It is contemplated that any probe used in the presentinvention can be labeled with any “reporter molecule,” so that isdetectable in any detection system, including, but not limited tofluorescent, enzyme (e.g., ELISA, as well as enzyme-based histochemicalassays), radioactive, quantum dots, and luminescent systems. It is notintended that the present invention be limited to any particulardetection system or label.

The term “template,” refers to nucleic acid that is to acted upon, suchas nucleic acid that is to be mixed with polymerase. In some cases“template” is sought to be sorted out from other nucleic acid sequences.“Substantially single-stranded template” is nucleic acid that is eithercompletely single-stranded (having no double-stranded areas) orsingle-stranded except for a proportionately small area ofdouble-stranded nucleic acid (such as the area defined by a hybridizedprimer or the area defined by intramolecular bonding). “Substantiallydouble-stranded template” is nucleic acid that is either completelydouble-stranded (having no single-stranded region) or double-strandedexcept for a proportionately small area of single-stranded nucleic acid.

III. Sequencing Apparatuses

A. Basic Features of the Apparatuses

The apparatuses comprise microfabricated channels to whichpolynucleotide templates to be sequenced are attached. Optionally, theapparatuses comprise plumbing components (e.g., pumps, valves, andconnecting channels) for flowing reaction reagents. The apparatuses canalso comprise an array of reservoirs for storing reaction reagents(e.g., the polymerase, each type of nucleotides, and other reagents caneach be stored in a different reservoir).

The microfabricated components of the apparatuses all have a basic “flowchannel” structure. The term “flow channel” or “microfabricated flowchannel” refers to recess in a structure which can contain a flow offluid or gas. The polynucleotide templates are attached to the interiorsurface of microfabricated channels in which synthesis occurs. Forconsistency and clarity, the flow channels are termed “synthesischannel” when referring to such specific use. The microfabricated flowchannels can also be actuated to function as the plumbing components(e.g., micro-pumps, micro-valves, or connecting channels) of theapparatuses.

In some applications, microfabricated flow channels are cast on a chip(e.g., a elastomeric chip). Synthesis channels are formed by bonding thechip to a flat substrate (e.g., a glass cover slip) which seals thechannel. Thus, one side of the synthesis channel is provided by the flatsubstrate. Typically, the polynucleotide templates are attached to theinterior surface of the substrate within the synthesis channel.

The plumbing components can be microfabricated as described in thepresent invention. For example, the apparatuses can contain in anintegrated system a flow cell in which a plurality of synthesis channelsare present, and fluidic components (such as micro-pumps, micro-valves,and connecting channels) for controlling the flow of the reagents intoand out of the flow cell. Alternatively, the sequencing apparatuses ofthe present invention utilize plumbing devices described in, e.g.,Zdeblick et al., A Microminiature Electric-to-Fluidic Valve, Proceedingsof the 4th International Conference on Solid State Transducers andActuators, 1987; Shoji et al., Smallest Dead Volume Microvalves forIntegrated Chemical Analyzing Systems, Proceedings of Transducers '91,San Francisco, 1991; Vieider et al., A Pneumatically Actuated MicroValve with a Silicon Rubber Membrane for Integration with Fluid HandlingSystems, Proceedings of Transducers '95, Stockholm, 1995.

As noted above, at least some of the components of the apparatuses aremicrofabricated. Employment of microfabricated synthesis channels and/ormicrofabricated plumbing components significantly reduce the dead volumeand decrease the amount of time needed to exchange reagents, which inturn increase the throughput. Microfabrication refers to featuredimensions on the micron level, with at least one dimension of themicrofabricated structure being less than 1000 μm. In some apparatuses,only the synthesis channels are microfabricated. In some apparatuses, inaddition to the synthesis channels, the valves, pumps, and connectingchannels are also microfabricated. Unless otherwise specified, thediscussion below of microfabrication is applicable to production of allmicrofabricated components of the sequencing apparatuses (e.g., thesynthesis channels in which sequencing reactions occur, and the valves,pumps, and connecting channels for controlling reagents flow to thesynthesis channels).

Various materials can be used to fabricate the microfabricatedcomponents (see, e.g., Unger et al., Science 288:113-116, 2000).Preferably, elastomeric materials are used. Thus, in some apparatuses,the integrated (i.e., monolithic) microstructures are made out ofvarious layers of elastomer bonded together. By bonding these variouselastomeric layers together, the recesses extending along the variouselastomeric layers form flow channels through the resulting monolithic,integral elastomeric structure.

In general, the microfabricated structures (e.g., synthesis channels,pumps, valves, and connecting channels) have widths of about 0.01 to1000 microns, and a width-to-depth ratios of between 0.1:1 to 100:1.Preferably, the width is in the range of 10 to 200 microns, awidth-to-depth ratio of 3:1 to 15:1.

B. Microfabrication with Elastomeric Materials

1. Basic Methods of Microfabrication

Various methods can be used to produce the microfabricated components ofthe sequencing apparatuses of the present invention. Fabrication of themicrochannels, valves, pumps can be performed as described in Unger etal., Science 288:113-116, 2000, which is incorporated herein byreference. In some methods (FIGS. 1 to 7B, pre-cured elastomer layersare assembled and bonded to produce a flow channel. As illustrated inFIG. 1, a first micro-machined mold 10 is provided. Micro-machined mold10 can be fabricated by a number of conventional silicon processingmethods, including but not limited to photolithography, ion-milling, andelectron beam lithography. The micro-machined mold 10 has a raised lineor protrusion 11 extending therealong. A first elastomeric layer 20 iscast on top of mold 10 such that a first recess 21 can be formed in thebottom surface of elastomeric layer 20, (recess 21 corresponding indimension to protrusion 11), as shown.

As can be seen in FIG. 2, a second micro-machined mold 12 having araised protrusion 13 extending therealong is also provided. A secondelastomeric layer 22 is cast on top of mold 12, as shown, such that arecess 23 can be formed in its bottom surface corresponding to thedimensions of protrusion 13.

As can be seen in the sequential steps illustrated in FIGS. 3 and 4,second elastomeric layer 22 is then removed from mold 12 and placed ontop of first elastomeric layer 20. As can be seen, recess 23 extendingalong the bottom surface of second elastomeric layer 22 forms a flowchannel 32.

Referring to FIG. 5, the separate first and second elastomeric layers 20and 22 (FIG. 4) are then bonded together to form an integrated (i.e.:monolithic) elastomeric structure 24.

As can been seen in the sequential step of FIGS. 6 and 7A, elastomericstructure 24 is then removed from mold 10 and positioned on top of aplanar substrate 14. As can be seen in FIGS. 7A and 7B, when elastomericstructure 24 has been sealed at its bottom surface to planar substrate14, recess 21 forms a flow channel 30.

The present elastomeric structures form a reversible hermetic seal withnearly any smooth planar substrate. An advantage to forming a seal thisway is that the elastomeric structures can be peeled up, washed, andre-used. In some apparatuses, planar substrate 14 is glass. A furtheradvantage of using glass is that glass is transparent, allowing opticalinterrogation of elastomer channels and reservoirs. Alternatively, theelastomeric structure can be bonded onto a flat elastomer layer by thesame method as described above, forming a permanent and high-strengthbond. This can prove advantageous when higher back pressures are used.

In some methods, microfabrication involves curing each layer ofelastomer “in place” (FIGS. 8 to 18). In these methods, flow and controlchannels arc defined by first patterning sacrificial layer on thesurface of an elastomeric layer (or other substrate, which can includeglass) leaving a raised line of sacrificial layer where a channel isdesired. Next, a second layer of elastomer is added thereover and asecond sacrificial layer is patterned on the second layer of elastomerleaving a raised line of sacrificial layer where a channel is desired. Athird layer of elastomer is deposited thereover. Finally, thesacrificial layer is removed by dissolving it out of the elastomer withan appropriate solvent, with the voids formed by removal of thesacrificial layer becoming the flow channels passing through thesubstrate.

Referring first to FIG. 8, a planar substrate 40 is provided. A firstelastomeric layer 42 is then deposited and cured on top of planarsubstrate 40. Referring to FIG. 9, a first sacrificial layer 44A is thendeposited over the top of elastomeric layer 42. Referring to FIG. 10, aportion of sacrificial layer 44A is removed such that only a first lineof sacrificial layer 44B remains as shown. Referring to FIG. 11, asecond elastomeric layer 46 is then deposited over the top of firstelastomeric layer 42 and over the first line of sacrificial layer 44B asshown, thereby encasing first line of sacrificial layer 44B betweenfirst elastomeric layer 42 and second elastomeric layer 46. Referring toFIG. 12, elastomeric layers 46 is then cured on layer 42 to bond thelayers together to form a monolithic elastomeric substrate 45.

Referring to FIG. 13, a second sacrificial layer 48A is then depositedover elastomeric structure 45. Referring to FIG. 14, a portion of secondsacrificial layer 48A is removed, leaving only a second sacrificiallayer 48B on top of elastomeric structure 45 as shown. Referring to FIG.15, a third elastomeric layer 50 is then deposited over the top ofelastomeric structure 45 (comprised of second elastomeric layer 42 andfirst line of sacrificial layer 44B) and second sacrificial layer 48B asshown, thereby encasing the second line of sacrificial layer 48B betweenelastomeric structure 45 and third elastomeric layer 50.

Referring to FIG. 16, third elastomeric layer 50 and elastomericstructure 45 (comprising first elastomeric layer 42 and secondelastomeric layer 46 bonded together) is then bonded together forming amonolithic elastomeric structure 47 having sacrificial layers 44B and48B passing therethrough as shown. Referring to FIG. 17, sacrificiallayers 44B and 48B are then removed (for example, by an solvent) suchthat a first flow channel 60 and a second flow channel 62 are providedin their place, passing through elastomeric structure 47 as shown.Lastly, referring to FIG. 18, planar substrate 40 can be removed fromthe bottom of the integrated monolithic structure.

2. Multilayer Construction

Soft lithographic bonding can be used to construct an integrated systemwhich contains multiple flow channels. A heterogenous bonding can beused in which different layers are of different chemistries. Forexample, the bonding process used to bind respective elastomeric layerstogether can comprise bonding together two layers of RTV 615 silicone.RTV 615 silicone is a two-part addition-cure silicone rubber. Part Acontains vinyl groups and catalyst; part B contains silicon hydride(Si—H) groups. The conventional ratio for RTV 615 is 10A:1B. Forbonding, one layer can be made with 30A:1B (i.e. excess vinyl groups)and the other with 3A:1B (i.e. excess Si—H groups). Each layer is curedseparately. When the two layers are brought into contact and heated atelevated temperature, they bond irreversibly forming a monolithicelastomeric substrate.

A homogenous bonding can also be used in which all layers are of thesame chemistry. For example, elastomeric structures are formed utilizingSylgard 182, 184 or 186, or aliphatic urethane diacrylates such as (butnot limited to) Ebecryl 270 or Irr 245 from UCB Chemical. For example,two-layer elastomeric structures were fabricated from pure acrylatedUrethane Ebe 270. A thin bottom layer was spin coated at 8000 rpm for 15seconds at 170° C. The top and bottom layers were initially cured underultraviolet light for 10 minutes under nitrogen utilizing a Model ELC500 device manufactured by Electrolite corporation. The assembled layerswere then cured for an additional 30 minutes. Reaction was catalyzed bya 0.5% vol/vol mixture of Irgacure 500 manufactured by Ciba-GeigyChemicals. The resulting elastomeric material exhibited moderateelasticity and adhesion to glass.

In some applications, two-layer elastomeric structures were fabricatedfrom a combination of 25% Ebe 270/50% Irr 245/25% isopropyl alcohol fora thin bottom layer, and pure acrylated Urethane Ebe 270 as a top layer.The thin bottom layer was initially cured for 5 min, and the top layerinitially cured for 10 minutes, under ultraviolet light under nitrogenutilizing a Model ELC 500 device manufactured by Electrolitecorporation. The assembled layers were then cured for an additional 30minutes. Reaction was catalyzed by a 0.5% vol/vol mixture of Irgacure500 manufactured by Ciba-Geigy Chemicals. The resulting elastomericmaterial exhibited moderate elasticity and adhered to glass.

Where encapsulation of sacrificial layers is employed to fabricate theelastomer structure as described above in FIGS. 8-18, bonding ofsuccessive elastomeric layers can be accomplished by pouring uncuredelastomer over a previously cured elastomeric layer and any sacrificialmaterial patterned thereupon. Bonding between elastomer layers occursdue to interpenetration and reaction of the polymer chains of an uncuredelastomer layer with the polymer chains of a cured elastomer layer.Subsequent curing of the elastomeric layer creates a bond between theelastomeric layers and create a monolithic elastomeric structure.

Referring to the first method of FIGS. 1 to 7B, first elastomeric layer20 can be created by spin-coating an RTV mixture on microfabricated mold12 at 2000 rpm's for 30 seconds yielding a thickness of approximately 40microns. Second elastomeric layer 22 can be created by spin-coating anRTV mixture on microfabricated mold 11. Both layers 20 and 22 can beseparately baked or cured at about 80° C. for 1.5 hours. The secondelastomeric layer 22 can be bonded onto first elastomeric layer 20 atabout 80° C. for about 1.5 hours.

Micromachined molds 10 and 12 can be patterned sacrificial layer onsilicon wafers. In an exemplary aspect, a Shipley SJR 5740 sacrificiallayer was spun at 2000 rpm patterned with a high resolution transparencyfilm as a mask and then developed yielding an inverse channel ofapproximately 10 microns in height. When baked at approximately 200° C.for about 30 minutes, the sacrificial layer reflows and the inversechannels become rounded. In preferred aspects, the molds can be treatedwith trimethylchlorosilane (TMCS) vapor for about a minute before eachuse in order to prevent adhesion of silicone rubber.

3. Suitable Materials

Allcock et al, Contemporary Polymer Chemistry, 2^(nd) Ed. describeselastomers in general as polymers existing at a temperature betweentheir glass transition temperature and liquefaction temperature.Elastomeric materials exhibit elastic properties because the polymerchains readily undergo torsional motion to permit uncoiling of thebackbone chains in response to a force, with the backbone chainsrecoiling to assume the prior shape in the absence of the force. Ingeneral, elastomers deform when force is applied, but then return totheir original shape when the force is removed. The elasticity exhibitedby elastomeric materials can be characterized by a Young's modulus.Elastomeric materials having a Young's modulus of between about 1 Pa-1TPa, more preferably between about 10 Pa-100 GPa, more preferablybetween about 20 Pa-1 GPa, more preferably between about 50 Pa-10 MPa,and more preferably between about 100 Pa-1 MPa are useful in accordancewith the present invention, although elastomeric materials having aYoung's modulus outside of these ranges could also be utilized dependingupon the needs of a particular application.

The systems of the present invention can be fabricated from a widevariety of elastomers. For example, elastomeric layers 20, 22, 42, 46and 50 can preferably be fabricated from silicone rubber. In someapplications, microstructures of the present systems are fabricated froman elastomeric polymer such as GE RTV 615 (formulation), a vinyl-silanecrosslinked (type) silicone elastomer (family). An important requirementfor the preferred method of fabrication is the ability to bond multiplelayers of elastomers together. In the case of multilayer softlithography, layers of elastomer are cured separately and then bondedtogether. This scheme requires that cured layers possess sufficientreactivity to bond together. Either the layers can be of the same type,and are capable of bonding to themselves, or they can be of twodifferent types, and are capable of bonding to each other. Otherpossibilities include the use an adhesive between layers and the use ofthermoset elastomers.

Given the tremendous diversity of polymer chemistries, precursors,synthetic methods, reaction conditions, and potential additives, thereare a huge number of possible elastomer systems that could be used tomake monolithic elastomeric microstructures. Variations in the materialsused most likely are driven by the need for particular materialproperties, i.e. solvent resistance, stiffness, gas permeability, ortemperature stability.

Common elastomeric polymers include, but are not limited to,polyisoprene, polybutadiene, polychloroprene, polyisobutylene,poly(styrene-butadiene-styrene), the polyurethanes, and silicones. Thefollowing is a non-exclusive list of elastomeric materials which can beutilized in connection with the present invention: polyisoprene,polybutadiene, polychloroprene, polyisobutylene,poly(styrene-butadiene-styrene), the polyurethanes, and siliconepolymers; or poly(bis(fluoroalkoxy)phosphazene) (PNF, Eypel-F),poly(carborane-siloxanes) (Dexsil), poly(acrylonitrile-butadiene)(nitrile rubber), poly(1-butene),poly(chlorotrifluoroethylene-vinylidene fluoride) copolymers (Kel-F),poly(ethyl vinyl ether), poly(vinylidene fluoride), poly(vinylidenefluoride-hexafluoropropylene) copolymer (Viton), elastomericcompositions of polyvinylchloride (PVC), polysulfone, polycarbonate,polymethylmethacrylate (PMMA), and polytertrafluoroethylene (Teflon).

In addition, polymers incorporating materials such as chlorosilanes ormethyl-, ethyl-, and phenylsilanes, and polydimethylsiloxane (PDMS) suchas Dow Chemical Corp. Sylgard 182, 184 or 186, or aliphatic urethanediacrylates such as (but not limited to) Ebecryl 270 or Irr 245 from UCBChemical can also be used.

In some methods, elastomers can also be “doped” with uncrosslinkablepolymer chains of the same class. For instance RTV 615 can be dilutedwith GE SF96-50 Silicone Fluid. This serves to reduce the viscosity ofthe uncured elastomer and reduces the Young's modulus of the curedelastomer. Essentially, the crosslink-capable polymer chains are spreadfurther apart by the addition of “inert” polymer chains, so this iscalled “dilution”. RTV 615 cures at up to 90% dilution, with a dramaticreduction in Young's modulus.

Other examples of doping of elastomer material can include theintroduction of electrically conducting or magnetic species. Should itbe desired, doping with fine particles of material having an index ofretraction different than the elastomeric material (i.e. silica,diamond, sapphire) is also contemplated as a system for altering therefractive index of the material. Strongly absorbing or opaque particlescan be added to render the elastomer colored or opaque to incidentradiation. This can conceivably be beneficial in an opticallyaddressable system.

4. Dimensions of the Microfabricated Structures

Some flow channels (30, 32, 60 and 62) preferably have width-to-depthratios of about 10:1. A non-exclusive list of other ranges ofwidth-to-depth ratios in accordance with the present invention is 0.1:1to 100:1, more preferably 1:1 to 50:1, more preferably 2:1 to 20:1, andmost preferably 3:1 to 15:1. In an exemplary aspect, flow channels 30,32, 60 and 62 have widths of about 1 to 1000 microns. A non-exclusivelist of other ranges of widths of flow channels in accordance with thepresent invention is 0.01 to 1000 microns, more preferably 0.05 to 1000microns, more preferably 0.2 to 500 microns, more preferably 1 to 250microns, and most preferably 10 to 200 microns. Exemplary channel widthsinclude 0.1 μm, 1 μm, 2 μm, 5 μm, 10 μm, 20 μm, 30 μm, 40 μm, 50 μm, 60μm, 70 μm, 80 μm, 90 μm, 100 μm, 110 μm, 120 μm, 130 μm, 140 μm, 150 μm,160 μm, 170 μm, 180 μm, 190 μm, 200 μm, 210 μm, 220 μm, 230 μm, 240 μm,and 250 μm.

Flow channels 30, 32, 60, and 62 have depths of about 1 to 100 microns.A non-exclusive list of other ranges of depths of flow channels inaccordance with the present invention is 0.01 to 1000 microns, morepreferably 0.05 to 500 microns, more preferably 0.2 to 250 microns, andmore preferably 1 to 100 microns, more preferably 2 to 20 microns, andmost preferably 5 to 10 microns. Exemplary channel depths includeincluding 0.01 μm, 0.02 μm, 0.05 μm, 0.1 μm, 0.2 μm, 0.5 μm, 1 μm, 2 μm,3 μm, 4 μm, 5 μm, 7.5 μm, 10 μm, 12.5 μm, 15 μm, 17.5 μm, 20 μm, 22.5μm, 25 μm, 30 μm, 40 μm, 50 μm, 75 μm, 100 μm, 150 μm, 200 μm, and 250μm.

The flow channels are not limited to these specific dimension ranges andexamples given above, and can vary in width in order to affect themagnitude of force required to deflect the membrane as discussed atlength below in conjunction with FIG. 21. For example, extremely narrowflow channels having a width on the order of 0.01 μm can be useful inoptical and other applications, as discussed in detail below.Elastomeric structures which include portions having channels of evengreater width than described above are also contemplated by the presentinvention, and examples of applications of utilizing such wider flowchannels include fluid reservoir and mixing channel structures.

Elastomeric layer 22 can be cast thick for mechanical stability. In anexemplary embodiment, layer 22 is 50 microns to several centimetersthick, and more preferably approximately 4 mm thick. A nonexclusive listof ranges of thickness of the elastomer layer in accordance with otherembodiments of the present invention is between about 0.1 micron to 10cm, 1 micron to 5 cm, 10 microns to 2 cm, 100 microns to 10 mm.

Accordingly, membrane 25 of FIG. 7B separating flow channels 30 and 32has a typical thickness of between about 0.01 and 1000 microns, morepreferably 0.05 to 500 microns, more preferably 0.2 to 250, morepreferably 1 to 100 microns, more preferably 2 to 50 microns, and mostpreferably 5 to 40 microns. As such, the thickness of elastomeric layer22 is about 100 times the thickness of elastomeric layer 20. Exemplarymembrane thicknesses include 0.01 μm, 0.02 μm, 0.03 μm, 0.05 μm, 0.1 μm,0.2 μm, 0.3 μm, 0.5 μm, 1 μm, 2 μm, 3 μm70 μm, 5 μm, 7.5 μm, 10 μm, 12.5μm, 15 μm, 17.5 μm, 20 μm, 22.5 μm, 25 μm, 30 μm, 40 μm, 50 μm, 75 μm,100 μm, 150 μm, 200 μm, 250 μm, 300 μm, 400 μm, 500 μm, 750 μm, and 1000μm

Similarly, first elastomeric layer 42 can have a preferred thicknessabout equal to that of elastomeric layer 20 or 22; second elastomericlayer 46 can have a preferred thickness about equal to that ofelastomeric layer 20; and third elastomeric layer 50 can have apreferred thickness about equal to that of elastomeric layer 22.

C. Operation of the Microfabricated Components

FIGS. 7B and 7C together show the closing of a first flow channel bypressurizing a second flow channel, with FIG. 7B (a front sectional viewcutting through flow channel 32 in corresponding FIG. 7A), showing anopen first flow channel 30; with FIG. 7C showing first flow channel 30closed by pressurization of the second flow channel 32. Referring toFIG. 7B, first flow channel 30 and second flow channel 32 are shown.Membrane separates the flow channels, forming the top of first flowchannel 30 and the bottom of second flow channel 32. As can be seen,flow channel 30 is “open”.

As can be seen in FIG. 7C, pressurization of flow channel 32 (either bygas or liquid introduced therein) causes membrane 25 to deflectdownward, thereby pinching off flow F passing through flow channel 30.Accordingly, by varying the pressure in channel 32, a linearly actuablevalving system is provided such that flow channel 30 can be opened orclosed by moving membrane 25 as desired.

It is to be understood that exactly the same valve opening and closingmethods can be achieved with flow channels 60 and 62. Since such valvesare actuated by moving the roof of the channels themselves (i.e., movingmembrane 25), valves and pumps produced by this technique have a trulyzero dead volume, and switching valves made by this technique have adead volume approximately equal to the active volume of the valve, forexample about 100×100×10 μm=100 pL. Such dead volumes and areas consumedby the moving membrane are approximately two orders of magnitude smallerthan known conventional microvalves. Smaller and larger valves andswitching valves are contemplated in the present invention, and anon-exclusive list of ranges of dead volume includes 1 aL to 1 uL, 100aL to 100 nL, 1 fL to 10 nL, 100 fL to 1 nL, and 1 pL to 100 pL

The extremely small volumes capable of being delivered by pumps andvalves in accordance with the present invention represent a substantialadvantage. Specifically, the smallest known volumes of fluid capable ofbeing manually metered is around 0.1 μl. The smallest known volumescapable of being metered by automated systems is about ten-times larger(1 μl). Utilizing pumps and valves of the present invention, volumes ofliquid of 10 nl or smaller can routinely be metered and dispensed. Theaccurate metering of extremely small volumes of fluid enabled by thepresent invention would be extremely valuable in a large number ofbiological applications, including diagnostic tests and assays.

FIGS. 21a and 21 b illustrate valve opening vs. applied pressure for a100 μM wide first flow channel 30 and a 50 μm wide second flow channel32. The membrane of this device was formed by a layer of GeneralElectric Silicones RTV 615 having a thickness of approximately 30 μm anda Young's modulus of approximately 750 kPa. FIGS. 21a and 21 b show theextent of opening of the valve to be substantially linear over most ofthe range of applied pressures.

Air pressure was applied to actuate the membrane of the device through a10 cm long piece of plastic tubing having an outer diameter of 0.025″connected to a 25 mm piece of stainless steel hypodermic tubing with anouter diameter of 0.025″ and an inner diameter of 0.013″. This tubingwas placed into contact with the control channel by insertion into theelastomeric block in a direction normal to the control channel. Airpressure was applied to the hypodermic tubing from an external LHDAminiature solenoid valve manufactured by Lee Co.

The response of valves of the present invention is almost perfectlylinear over a large portion of its range of travel, with minimalhysteresis. While valves and pumps do not require linear actuation toopen and close, linear response does allow valves to more easily be usedas metering devices. In some applications, the opening of the valve isused to control flow rate by being partially actuated to a known degreeof closure. Linear valve actuation makes it easier to determine theamount of actuation force required to close the valve to a desireddegree of closure. Another benefit of linear actuation is that the forcerequired for valve actuation can be easily determined from the pressurein the flow channel. If actuation is linear, increased pressure in theflow channel can be countered by adding the same pressure (force perunit area) to the actuated portion of the valve.

D. Schematic Illustration of the Elastomeric Apparatuses

An exemplary sequencing system is illustrated in FIG. 25. Fourreservoirs 150A, 150B, 150C and 150D have labeled nucleotides A, C, Tand G respectively disposed therein. Four flow channels 30A, 30B, 30Cand 30D are connected to reservoirs 150A, 150B, 150C and 150D. Fourcontrol lines 32A, 32B, 32C and 32D (shown in phantom) are disposedthereacross with control line 32A permitting flow only through flowchannel 30A (i.e.: sealing flow channels 30B, 30C and 30D), when controlline 32A is pressurized. Similarly, control line 32B permits flow onlythrough flow channel 30B when pressurized. As such, the selectivepressurization of control lines 32A, 32B, 32C and 32D sequentiallyselects a desired nucleotide (A, C, T or G) from a desired reservoir(150A, 150B, 150C or 150D). The fluid then passes through flow channel120 into a multiplexed channel flow controller 125, which in turndirects fluid flow into one or more of a plurality of synthesis channelsor reaction chambers 122A, 122B, 122C, 122D or 122E in which solid phasesynthesis can be carried out.

FIG. 26 illustrates a further extension of the system shown in FIG. 25.It has a plurality of reservoirs R1 to R13. These reservoirs can containthe labeled nucleotides, nucleotide polymerase, or reagents for coatingthe surface of the synthesis channel and attaching polynucleotidetemplates (see below for further discussion). The reservoirs areconnected to systems 200 as set forth in FIG. 25. Systems 200 areconnected to a multiplexed channel flow controller 125, which is in turnconnected to a plurality of synthesis channels or reaction chambers. Anadvantage of this system is that both of multiplexed channel flowcontrollers 125 and fluid selection systems 200 can be controlled by thesame pressure inputs 170 and 172, provided a “close horizontal” and a“close vertical” control lines (160 and 162, in phantom) are alsoprovided.

Some apparatuses comprise a plurality of selectively addressablereaction chambers that are disposed along a flow channel. In theseapparatuses, the polynucleotide templates can be attached to the surfaceof the reaction chambers instead of the surface of flow channels. Anexemplary embodiment of such apparatuses is illustrated in FIGS. 22A,22B, 22C and 22D. It is a system for selectively directing fluid flowinto one or more of a plurality of reaction chambers disposed along aflow channel.

FIG. 22A shows a top view of a flow channel 30 having a plurality ofreaction chambers 80A and 80B disposed therealong. Preferably flowchannel 30 and reaction chambers 80A and 80B are formed together asrecesses into the bottom surface of a first layer 100 of elastomer.

FIG. 22B shows a bottom plan view of another elastomeric layer 110 withtwo control lines 32A and 32B each being generally narrow, but havingwide extending portions 33A and 33B formed as recesses therein.

As seen in the exploded view of FIG. 22C, and assembled view of FIG.22D, elastomeric layer 110 is placed over elastomeric layer 100. Layers100 and 110 are then bonded together, and the integrated system operatesto selectively direct fluid flow F (through flow channel 30) into eitheror both of reaction chambers 80A and 80B, as follows. Pressurization ofcontrol line 32A will cause the membrane 25 (i.e.: the thin portion ofelastomer layer 100 located below extending portion 33A and over regions82A of reaction chamber 80A) to become depressed, thereby shutting offfluid flow passage in regions 82A, effectively sealing reaction chamber80 from flow channel 30. As can also be seen, extending portion 33A iswider than the remainder of control line 32A. As such, pressurization ofcontrol line 32A will not result in control line 32A sealing flowchannel 30.

As can be appreciated, either or both of control lines 32A and 32B canbe actuated at once. When both control lines 32A and 32B are pressurizedtogether, sample flow in flow channel 30 will enter neither of reactionchambers 80A or 80B.

The concept of selectably controlling fluid introduction into variousaddressable reaction chambers disposed along a flow line (FIG. 22) canbe combined with concept of selectably controlling fluid flow throughone or more of a plurality of parallel flow lines (FIG. 21) to yield asystem in which a fluid sample or samples can be sent to any particularreaction chamber in an array of reaction chambers. An example of such asystem is provided in FIG. 23, in which parallel control channels 32A,32B and 32C with extending portions 34 (all shown in phantom)selectively direct fluid flows F1 and F2 into any of the array ofreaction wells 80A, 80B, 80C or 80D as explained above; whilepressurization of control lines 32C and 32D selectively shuts off flowsF2 and F1, respectively.

In yet another embodiment, fluid passage between parallel flow channelsis possible. Referring to FIG. 24, either or both of control lines 32Aor 32D can be depressurized such that fluid flow through lateralpassageways 35 (between parallel flow-channels 30A and 30B) ispermitted. In this aspect of the invention, pressurization of controllines 32C and 32D would shut flow channel 30A between 35A and 35B, andwould also shut lateral passageways 35B. As such, flow entering as flowF1 would sequentially travel through 30A, 35A and leave 30B as flow F4.

E. Non-elastomer Based Apparatuses

As discussed above, while elastomers are preferred materials forfabricating the sequencing apparatuses of the present invention,non-elastomer based microfluidic devices can also be used in theapparatuses of the present invention. In some applications, thesequencing apparatuses utilize microfluidics based on conventionalmicro-electro-mechanical system (MEMS) technology. Methods of producingconventional MEMS microfluidic systems such as bulk micro-machining andsurface micro-machining have been described, e.g., in Terry et al., AGas Chromatographic Air Analyzer Fabricated on a Silicon Wafer, IEEETrans. on Electron Devices, v. ED-26, pp. 1880-1886, 1979; and Berg etal., Micro Total Analysis Systems, New York, Kluwer, 1994.

Bulk micro-machining is a subtractive fabrication method whereby singlecrystal silicon is lithographically patterned and then etched to formthree-dimensional structures. For example, bulk micromachiningtechnology, which includes the use of glass wafer processing,silicon-to-glass wafer bonding, has been commonly used to fabricateindividual microfluidic components. This glass-bonding technology hasalso been used to fabricate microfluidic systems.

Surface micro-machining is an additive method where layers ofsemiconductor-type materials such as polysilicon, silicon nitride,silicon dioxide, and various metals are sequentially added and patternedto make three-dimensional structures. Surface micromachining technologycan be used to fabricate individual fluidic components as well asmicrofluidic systems with on-chip electronics. In addition, unlikebonded-type devices, hermetic channels can be built in a relativelysimple manner using channel walls made of polysilicon (see, e.g.,Webster et al., Monolithic Capillary Gel Electrophoresis Stage withOn-Chip Detector, in International Conference on Micro ElectromechanicalSystems, MEMS 96, pp. 491-496, 1996), silicon nitride (see, e.g.,Mastrangelo et al., Vacuum-Sealed Silicon Micromachined IncandescentLight Source, in Intl. Electron Devices Meeting, IDEM 89, pp. 503-506,1989), and silicon dioxide.

In some applications, electrokinetic flow based microfluidics can beemployed in the sequencing apparatuses of the present invention.Briefly, these systems direct reagents flow within an interconnectedchannel and/or chamber containing structure through the application ofelectrical fields to the reagents. The electrokinetic systemsconcomitantly regulate voltage gradients applied across at least twointersecting channels. Such systems are described, e.g., in WO 96/04547and U.S. Pat. No. 6,107,044.

An exemplary electrokinetic flow based microfluidic device can have abody structure which includes at least two intersecting channels orfluid conduits, e.g., interconnected, enclosed chambers, which channelsinclude at least three unintersected termini. The intersection of twochannels refers to a point at which two or more channels are in fluidcommunication with each other, and encompasses “T” intersections, crossintersections, “wagon wheel” intersections of multiple channels, or anyother channel geometry where two or more channels are in such fluidcommunication. An unintersected terminus of a channel is a point atwhich a channel terminates not as a result of that channel'sintersection with another channel, e.g., a “T” intersection.

In some electrokinetic flow based apparatuses, at least threeintersecting channels having at least four unintersected termini arepresent. In a basic cross channel structure, where a single horizontalchannel is intersected and crossed by a single vertical channel,controlled electrokinetic transport operates to direct reagent flowthrough the intersection, by providing constraining flows from the otherchannels at the intersection. Simple electrokinetic flow of this reagentacross the intersection could be accomplished by applying a voltagegradient across the length of the horizontal channel, i.e., applying afirst voltage to the left terminus of this channel, and a second, lowervoltage to the right terminus of this channel, or by allowing the rightterminus to float (applying no voltage).

In some other applications, the apparatus comprises a microfabricatedflow cell with external mini-fluidics. Such an apparatus is illustratedin FIG. 27. The glass cover slip can be anodically bonded to the surfaceof the flow cell. The interrogation region is 100 μm×100 μm×100 μm,while the input and output channels are 100 μm×100 μm×100 μm. Holes forthe attachment of plumbing are etched at the ends of the channels. Forsuch apparatuses, the fluidics can be external. Plumbing can beperformed with standard HPLC components, e.g., from Upchurch andHamilton. In the interrogation region, the polynucleotide template isattached to the surface with standard avidin-biotin chemistry. Multiplecopies of templates can be attached to the apparatus. For example, for a7 kb template, the radius of gyration is approximately 0.2 μm.Therefore, about 10⁵ molecules can be attached while preventing themolecules from touching. Reagent switching can be accomplished with,e.g., an Upchurch six port injection valve and driven by, e.g., a TharDesigns motor. Fluid can be pumped with a syringe pump. The detectionsystem can be an external optical microscope, with the objective beingin close proximity to the glass cover slip.

IV Analysis of Polynucleotide Sequences

A. Template Preparation and Attachment to Surface of Synthesis Channel

1. The General Scheme

In some applications, the polynucleotides to be analyzed are firstcloned in single-stranded M13 plasmid (see, e.g., Current Protocols InMolecular Biology, Ausubel, et al., eds., John Wiley & Sons, Inc. 1995;and Sambrook, et al., Molecular Cloning. A Laboratory Manual, ColdSpring Harbor Press, 1989). The single stranded plasmid is primed by5′-biotinylated primers (see, e.g., U.S. Pat. No. 5,484,701), and doublestranded plasmid can then be synthesized. The double stranded circle isthen linearized, and the biotinylated strand is purified. In somemethods, templates of around 100 bp in length are analyzed. In somemethods, templates to be sequenced are about 1 kb in length. In othermethods, templates that can be analyzed have a length of about 3 kb, 10kb, or 20 kb.

Primer annealing is performed under conditions which are stringentenough to achieve sequence specificity yet sufficiently permissive toallow formation of stable hybrids at an acceptable rate. The temperatureand length of time required for primer annealing depend upon severalfactors including the base composition, length and concentration of theprimer, and the nature of the solvent used, e.g., the concentration ofDMSO, formamide, or glycerol, and counter ions such as magnesium.Typically, hybridization with synthetic polynucleotides is carried outat a temperature that is approximately 5 to 10° C. below the meltingtemperature of the target-primer hybrid in the annealing solvent.Preferably, the annealing temperature is in the range of 55 to 75° C.and the primer concentration is approximately 0.2 μM. Under thesepreferred conditions, the annealing reaction can be complete in only afew seconds.

The single stranded polynucleotide templates to be analyzed can be DNAor RNA. They can comprise naturally occurring and or non-naturallyoccurring nucleotides. Templates suitable for analysis according to thepresent invention can have various sizes. For example, the template canhave a length of 100 bp, 200 bp, 500 bp, 1 kb, 3 kb, 10 kb, or 20 kb.

In some methods, the templates are immobilized to the surface of thesynthesis channels (e.g., 122A-122E in FIG. 25). By immobilizing thetemplates, unincorporated nucleotides can be removed from the synthesischannels by a washing step. The templates can be immobilized to thesurface prior to hybridization to the primer. The templates can also behybridized to the primers first and then immobilize to the surface.Alternatively, the primers are immobilized to the surface, and thetemplates are attached to the synthesis channels through hybridizationto the primers.

Various methods can be used to immobilize the templates or the primersto the surface of the synthesis channels or reaction chambers. Theimmobilization can be achieved through direct or indirect bonding of thetemplates to the surface. The bonding can be by covalent linkage. See,Joos et al., Analytical Biochemistry 247:96-101, 1997; Oroskar et al.,Clin. Chem 42:1547-1555, 1996; and Khandjian, Mole. Bio. Rep.11:107-115, 1986. The bonding can also be through non-covalent linkage.For example, Biotin-streptavidin (Taylor et al., J. Phys. D. Appl. Phys.24:1443, 1991) and digoxigenin and anti-digoxigenin (Smith et al.,Science 253: 1122, 1992) are common tools for attaching polynucleotidesto surfaces and parallels. Alternatively, the bonding can be achieved byanchoring a hydrophobic chain into a lipidic monolayer or bilayer.

When biotin-streptavidin linkage is used to immobilize the templates,the templates are biotinylated, and one surface of the synthesischannels are coated with streptavidin. Since streptavidin is a tetramer,it has four biotin binding sites per molecule. Thus, in order to coat asurface with streptavidin, the surface can be biotinylated first, andthen one of the four binding sites of streptavidin can be used to anchorthe protein to the surface, leaving the other sites free to bind thebiotinylated template (see, Taylor et al., J. Phys. D. Appl. Phys.24:1443, 1991). Such treatment leads to a high density of streptavidinon the surface of the synthesis channel, allowing a correspondingly highdensity of template coverage. Reagents for biotinylating a surface canbe obtained, for example, from Vector laboratories.

In some applications, the substrate or synthesis channel is pretreatedto create surface chemistry that facilitates attachment of thepolynucleotide templates and subsequent synthesis reactions. In somemethods, the surface is coated with a polyelectrolyte multilayer (PEM).Attachment of templates to PEM-coated surface can be accomplished bylight-directed spatial attachment (see, e.g., U.S. Pat. Nos. 5,599,695,5,831,070, and 5,959,837). Alternatively, the templates can be attachedto PEM-coated surface entire chemically (see below for detail). In somemethods, non-PEM based surface chemistry can be created prior totemplate attachment.

2. Attachment of Diverse Templates to a Single Channel

While diverse polynucleotide templates can be each immobilized to andsequenced in a separate synthesis channel, multiple templates can alsobe sequenced in a single microfluidic synthesis channel. In the latterscenario, the templates are attached at different locations along theflow path of the channel. This can be accomplished by a variety ofdifferent methods, including hybridization of primer capture sequencesto oligonucleotides immobilized at different points on the substrate,and sequential activation of different points down the channel towardstemplate immobilization.

Methods of creation of surfaces with arrays of oligonucleotides havebeen described, e.g., in U.S. Pat. Nos. 5,744,305, 5,837,832, and6,077,674. Such a surface can be used as a substrate that is to be bondto a microfluidic chip and form the synthesis channel. Primers with twodomains, a priming domain and a capture domain, can be used to anchortemplates to the substrate. The priming domain is complementary to thetarget template. The capture domain is present on the non-extended sideof the priming sequence. It is not complementary to the target template,but rather to a specific oligonucleotide sequence present on thesubstrate. The target templates can be separately hybridized with theirprimers, or (if the priming sequences are different) simultaneouslyhybridized in the same solution. Incubation of the primer/templateduplexes in the flow channel under hybridization conditions allowsattachment of each template to a unique spot. Multiple synthesischannels can be charged with templates in this fashion simultaneously.

Another method for attaching multiple templates in a single channel isto sequentially activate portions of the substrate and attach templateto them. Activation of the substrate can be achieved by either opticalor electrical means. Optical illumination can be used to initiate aphotochemical deprotection reaction that allows attachment of thetemplate to the surface (see, e.g., U.S. Pat. Nos. 5,599,695, 5,831,070,and 5,959,837). For instance, the substrate surface can be derivatizedwith “caged biotin”, a commercially available derivative of biotin thatbecomes capable of binding to avidin only after being exposed to light.Templates can then be attached by exposure of a site to light, fillingth e channel with avidin solution, washing, and then flowingbiotinylated template into the channel. Another variation is to prepareavidinylated substrate and a template with a primer with a caged biotinmoiety; the template can then be immobilized by flowing into the channeland illumination of the solution above a desired area. Activatedtemplate/primer duplexes are then attached to the first wall theydiffused to, yielding a diffusion limited spot.

Electrical means can also be used to direct template to specific pointsin the channel. By positively charging one electrode in the channel andnegatively charging the others, a field gradient can be created whichdrives the template to a single electrode, where it can attach (see,e.g., U.S. Pat. Nos. 5,632,957, 6,051,380, and 6,071,394).Alternatively, it can be achieved by electrochemically activatingregions of the surface and changing the voltage applied to theelectrodes.

B. Exemplary Surface Chemistry for Attaching Templates: PEM Coating

In some methods, the surface of synthesis channels are coated with PEMprior to attachment of the templates (or primers). Such attachmentscheme can be both an ex-situ process or an in situ process. With theex-situ protocol, the surface of the flat substrate is coated with PEMfirst, followed by attachment of the templates. The elastomericmicrofluidic chip is then bonded to the substrate to form and seal thesynthesis channel. With the in-situ protocol, the microfluidic chip isattached to the flat substrate first, and a PEM is then constructed inthe channels. The templates are then attached inside the channels. Instill some other applications, the microfluidic chip can be bonded tothe flat substrate at any point in the template attachment process, andthe remaining steps can be completed inside the microfluidic channels.

Preferably, the in-situ protocol is used. The method described hereleads to low nonspecific binding of labeled (e.g., with fluorescent dye)nucleotides and good seal of the microfluidic components and thesynthesis channels. A good seal between the microfluidic components andthe synthesis channels allows the use of higher pressures, which in turnincreases flow rates and decreases exchange times. The various methodsfor attaching the templates to the surface of the synthesis channel arediscussed in detail below.

An exemplified scheme of the ex situ protocol is as follows. First, thesurface of a glass cover slip is cleaned and then coated with apolyelectrolyte multilayer (PEM). Following biotinylation of thecarboxylic acid groups, streptavidin is then applied to generate asurface capable of capturing biotinylated molecules. Biotinylatedpolynucleotide templates are then added to the coated glass cover slipfor attachment. The surface chemistry thus created is particularlysuited for sequencing by synthesis with fluorescent nucleotides, becauseit generates a strong negatively-charged surface which repels thenegatively-charged nucleotides. Detailed procedures for cleaning thecover slips, coating of polyelectrolyte multilayer, and attachment ofthe templates are described below.

PEM formation proceeds by the sequential addition of polycations andpolyanions, which are polymers with many positive or negative charges,respectively. Upon addition of a polycation to a negatively-chargedsurface, the polycation deposits on the surface, forming a thin polymerlayer and reversing the surface charge. Similarly, a polyanion depositedon a positively charged surface forms a thin layer of polymer and leavesa negatively charged surface. Alternating exposure to poly(+) andpoly(−) generates a polyelectrolyte multilayer structure with a surfacecharge determined by the last polyelectrolyte added; in the case ofincompletely-charged surfaces, multiple-layer deposition also tends toincrease surface charge to a well defined and stable level. PEMformation has been described by Decher et al.(Thin Solid Films,210:831-835, 1992).

Carboxylic acid groups are negatively charged at pH 7, and are a commontarget for covalent bond formation. By terminating the surface withcarboxylic acid groups, a surface which is both stronglynegatively-charged and chemically reactive can be generated Inparticular, amines can link to them to form amide bonds, a reaction thatcan be catalyzed by carbodiimides. A molecule with biotin at one end, ahydrophilic spacer, and an amine at the other end is used to terminatethe surface with biotin.

An avidin molecule is capable of binding up to four biotin molecules.This means that avidin, and its derivative Streptavidin, is capable ofconverting a biotin-terminated surface to a surface capable of capturingbiotin. Streptavidin, which carries a slight negative charge, is used toattach the polynucleotide templates to be analyzed to the surface byusing a biotinylated primer. A buffer with a high concentration ofmultivalent salt is used in order to screen the repulsion of thenegatively charged surface for the negatively-charged DNA.

To coat the polyelectrolyte multilayer, the glass cover slips are firstcleaned with HP H₂O (H₂O deionized to 18.3 MOhm-cm and filtered to 0.2μm) and a RCA Solution (6:4:1 mixture of HP H₂O, (30% NH₄OH), and (30%H₂O₂)). The cover slips are then sonicated in 2% Micro 90 detergent for20 minutes. After rinse thoroughly with HP H₂O, the cover slips arestirred in gently boiling RCA solution for at least 1 hour, and rinsedagain with HP H₂O.

After cleaning, the glass cover slips are submerged in PAll solution(Poly(allylamine) (PAll, +): 2 mg/ml in HP H₂O, adjusted to pH 7.0) andagitate for at least 10 minutes. The cover slips are then removed fromPAll and washed with HP H₂O by submerging in HP H₂O with agitation forat least three times. The treatment continues by agitation in a PAcrsolution (Poly(acrylic acid) (PAcr, −): 2 mg/ml in HP H₂O, adjusted topH 7.0) for at least 10 minutes and washing with HP H₂O. The treatmentsteps are then repeated once.

After PEM coating, the PEM coated glass is incubated with a EDC/BLCPAsolution for 30 minutes. The EDC/BLCPA solution is prepared by mixingequal amounts of 50 mM EDC solution (in MES buffer) and 50 mM BLCPA (inMES buffer) and diluting to 5 mM in MES buffer. The glass is then rinsedwith 10 mM Tris-NaCl and incubated with 0.1 mg/ml streptavidin solutionfor 1 hour. After washing with 10 mM Tris-NaCl, the glass is incubatedwith a solution containing the polynucleotide template (10⁻⁷ M in Tris100 mM MgCl₂) for 30 minutes. The glass is again rinsed thoroughly with10 mM Tris-NaCl.

For in-situ attachment, the microfluidic substrate is bonded to theglass cover slip by HCl-assisted bonding. Essentially, the chips arefirst washed with a surfactant (e.g., first with HP H₂O, then in 0.1%Tween 20, then rinse again with HP H₂O). The washed microfluidic chipsare then put on the glass cover slips with a few microliters of diluteHCl (e.g., 1% HCl in HP H₂O), followed by baking at 37° C. for 1-2hours. Such treatment enhances the bond strength to glass (e.g., >20 psipressure) without increasing nonspecific adsorption.

Following HCl treatment, PEM formation, biotinylation,streptavidinylation, and template attachment can be performed usingessentially the same reagents and methods as described above for ex-situattachment, except the solutions are injected through the channels bypressure instead of just being aliquoted onto the substrate surface.

Coating the microchannel surface with the PEM technique is significantfor analyzing polynucleotide sequences according to the presentinvention. In general, the method used to attach the template to thesurface should fulfill several requirements in order to be useful in asequencing-by-synthesis application. First, it must be possible toattach reasonable quantities of polynucleotide templates. In addition,the attached templates should remain active for polymerase action.Further, nonspecific binding of fluorescent nucleotides should be verylow.

If insufficient numbers of template molecules are bound, thesignal-to-noise ratio of the technique is too low to allow usefulsequencing. Binding large quantities of templates is insufficient,however, if the primer/target duplex cannot be extended by a polymerase.This is a problem for surface chemistry based on building offamine-bearing surfaces: amines are positively charged at normal pH. Thismeans that the negatively-charged DNA backbone can non-specificallystick to the surface, and that the polymerase is sterically impeded fromadding nucleotides. Finally, if there is significant nonspecific bindingof fluorescent nucleotides to the surface, it becomes impossible todistinguish between signal due to incorporation and signal due tononspecific binding.

When the nucleotides are fluorescently labeled, they generally haverelatively strong nonspecific binding to many surfaces because theypossess both a strongly polar moiety (the nucleotide, and in particularthe triphosphate) and a relatively hydrophobic moiety (the fluorescentdye). A surface bearing positively-charged groups (i.e. amines)invariably has a very high nonspecific binding due to the attraction ofthe triphosphate group (which is strongly negatively charged) to thepositively-charged amines. Neutral surfaces generally have strongnonspecific binding due to the action of the fluorescent nucleotide as asurfactant (i.e. assembling with nonpolar moiety towards the uncharged(more hydrophobic) surface and polar end in the aqueous phase). Asurface bearing negative charges can repel the negatively chargedfluorescent nucleotides, so it has the lowest nonspecific binding. Glassis such a surface, but the surface silanols that give it its negativecharge in water are a difficult target to attach DNA to directly.Typical DNA attachment protocols use silanization (often withaminosilanes) to attach template; as discussed earlier amino groups leadto unacceptable levels of nonspecific binding.

A polyelectrolyte multilayer terminated with carboxylic acid-bearingpolymer fulfills all three criteria First, it is easy to attachpolynucleotide to because carboxylic acids are good targets for covalentbond formation. Second, the attached template is active for extension bypolymerases—most probably, the repulsion of like charges prevents thetemplate from “laying down” on the surface. Finally, the negative chargerepels the fluorescent nucleotides, and nonspecific binding is low.

The attachment scheme described here is easy to generalize on. Withoutmodification, the PEM/biotin/streptavidin surface that is produced canbe used to capture or immobilize any biotinylated molecule. A slightmodification can be the use of another capture pair, i.e. substitutingdigoxygenin (dig) for biotin and labeling the molecule to be immobilizedwith anti-digoxygenin (anti-dig). Reagents for biotinylation ordig-labeling of amines are all commercially available.

Another generalization is that the chemistry is nearly independent ofthe surface chemistry of the support. Glass, for instance, can supportPEMs terminated with either positive or negative polymer, and a widevariety of chemistry for either. But other substrates such as silicone,polystyrene, polycarbonate, etc, which are not as strongly charged asglass, can still support PEMs. The charge of the final layer of PEMs onweakly-charged surfaces becomes as high as that of PEMs onstrongly-charged surfaces, as long as the PEM has sufficiently-manylayers. For example, PEM formation on O₂-plasma treated silicone rubberhas been demonstrated by the present inventors. This means that all theadvantages of the glass/PEM/biotin/Streptavidin/biotin-DNA surfacechemistry can be applied to other substrates.

Although the above discussion describes the immobilization ofpolynucleotide templates by attachment to the surface of flow channelsor the surface of reaction chambers disposed along flow channels, othermethods of template immobilization can also be employed in the methodsof the present invention. In some methods, the templates can be attachedto microbeads, which can be arranged within the microfluidic system. Forinstance, commercially-available latex microspheres with pre-definedsurface chemistry can be used. The polynucleotide templates can beattached either before or after the microbeads are inducted into themicrofluidic system. Attachment of template before beads are addedallows a reduction in system complexity and setup time (as manytemplates can be attached to different aliquots of beadssimultaneously). Attachment of template to beads in situ can alloweasier manipulation of surface chemistry (as bead surface chemistry canbe manipulated in bulk and externally to the microfluidic device). Beadsshould be held in place within the flow system for this technique to beeffective. Methods to achieve this include, e.g., flowing the beads intoorifices too small for them to flow through (where they would become“wedged in”), the creation of “microscreens” (i.e. barriers in thechannel with apertures too small for beads to pass through), andinsertion of the beads into hollows in the channels where they areaffixed by simple Van der Waals forces.

C. Primer Extension Reaction

Once templates are immobilized to the surfaces of synthesis channels,primer extension reactions are performed (E. D. Hyman, Anal. Biochem.,174, p. 423, 1988). If part of the template sequence is known, aspecific primer can be constructed and hybridized to the template.Alternatively, a linker can be ligated to the template of unknownsequence in order to allow for hybridization of a primer. The primer canbe hybridized to the template before or after immobilization of thetemplate to the surface of the synthesis channel.

In some methods, the primer is extended by a nucleic acid polymerase inthe presence of a single type of labeled nucleotide. Label isincorporated into the template/primer complex only if the labelednucleotide added to the reaction is complementary to the nucleotide onthe template adjacent the 3′ end of the primer. The template issubsequently washed to remove any unincorporated label, and the presenceof any incorporated label is determined. A radioactive label can bedetermined by counting or any other method known in the art, whilefluorescent labels can be induced to fluoresce, e.g., by excitation.

In some applications of the present invention, a combination of labeledand non-labeled nucleotides are used in the analysis. Because there aremultiple copies of each template molecule immobilized on the surface ofthe synthesis channel, a small percentage of labeled nucleotides issufficient for detection by a detection device (see below). For example,for fluorescently labeled nucleotides, the percentage of labelednucleotide can be less than 20%, less than 10%, less than 5%, less than1%, less than 0.1%, less than 0.01%, or even less than 0.001% of thetotal labeled and unlabeled nucleotides for each type of thenucleotides.

1. Labeled Nucleotides

In some methods, at least one and usually all types of thedeoxyribonucleotides (dATP, dTTP, dGTP, dCTP, dUTP/dTTP) or nucleotides(ATP, UTP, GTP, and CTP) are labeled. Various labels which are easilydetected include radioactive labels, optically detectable labels,spectroscopic labels and the like. Preferably, fluorescent labels areused. The different types of nucleotides can be labeled with the samekind of labels. Alternatively, a different kind of label can be used tolabel each different type of nucleotide.

In some methods, fluorescent labels are used. the fluorescent label canbe selected from any of a number of different moieties. The preferredmoiety is a fluorescent group for which detection is quite sensitive.For example, fluorescein- or rhodamine-labeled nucleotide triphosphatesare available (e.g., from NEN DuPont).

Fluorescently labeled nucleotide triphosphates can also be made byvarious fluorescence-labeling techniques, e.g., as described in Kambaraet al. (1988) “Optimization of Parameters in a DNA Sequenator UsingFluorescence Detection,” Bio/Technol. 6:816-821; Smith et al. (1985)Nucl. Acids Res, 13:2399-2412; and Smith et al. (1986) Nature321:674-679. Fluorescent labels exhibiting particularly highcoefficients of destruction can also be useful in destroying nonspecificbackground signals.

2. Blocking Agents:

In some methods during the primer extension step, a chain elongationinhibitor can be employed in the reaction (see, e.g., Dower et al., U.S.Pat. No. 5,902,723. Chain elongation inhibitors are nucleotide analogueswhich either are chain terminators which prevent further addition by thepolymerase of nucleotides to the 3′ end of the chain by becomingincorporated into the chain themselves. In some methods, the chainelongation inhibitors are dideoxynucleotides. Where the chain elongationinhibitors are incorporated into the growing polynucleotide chain, theyshould be removed after incorporation of the labeled nucleotide has beendetected, in order to allow the sequencing reaction to proceed usingdifferent labeled nucleotides. Some 3′ to 5′ exonucleases, e.g.,exonuclease III, are able to remove dideoxynucleotides.

Other than chain elongation inhibitors, a blocking agent or blockinggroup can be employed on the 3′ moiety of the deoxyribose group of thelabeled nucleotide to prevent nonspecific incorporation. Optimally, theblocking agent should be removable under mild conditions (e.g.,photosensitive, weak acid labile, or weak base labile groups), therebyallowing for further elongation of the primer strand with a nextsynthetic cycle. If the blocking agent also contains the fluorescentlabel, the dual blocking and labeling functions are achieved without theneed for separate reactions for the separate moieties. For example, thelabeled nucleotide can be labeled by attachment of a fluorescent dyegroup to the 3′ moiety of the deoxyribose group, and the label isremoved by cleaving the fluorescent dye from the nucleotide to generatea 3′ hydroxyl group. The fluorescent dye is preferably linked to thedeoxyribose by a linker arm which is easily cleaved by chemical orenzymatic means.

Examples of blocking agents include, among others, light sensitivegroups such as 6-nitoveratryloxycarbonyl (NVOC), 2-nitobenzyloxycarbonyl(NBOC), .α,.α-dimethyl-dimethoxybenzyloxycarbonyl (DDZ),5-bromo-7-nitroindolinyl, o-hydroxy-2-methyl cinnamoyl, 2-oxymethyleneanthraquinone, and t-butyl oxycarbonyl (TBOC). Other blocking reagentsare discussed, e.g., in U.S. Ser. No. 07/492,462; Patchornik (1970) J.Amer. Chem. Soc. 92:6333; and Amit et al. (1974) J. Org. Chem. 39:192.Nucleotides possessing various labels and blocking groups can be readilysynthesized. Labeling moieties are attached at appropriate sites on thenucleotide using chemistry and conditions as described, e.g., in Gait(1984) Oligonucleotide Synthesis: A Practical Approach, IRL Press,Oxford.

3. Polymerases

Depending on the template, either RNA polymerase or DNA polymerases canbe used in the primer extension. For analysis of DNA templates, many DNApolymerases are available. Examples of suitable DNA polymerases include,but are not limited to, Sequenase 2.0.RTM., T4 DNA polymerase or theKlenow fragment of DNA polymerase 1, or Vent polymerase. In somemethods, polymerases which lack 3′→5′ exonuclease activity can be used(e.g., T7 DNA polymerase (Amersham) or Klenow fragment of DNA polymeraseI (New England Biolabs)). In some methods, when it is desired that thepolymerase have proof-reading activity, polymerases lacking 3′→5′exonuclease activity are not used. In some methods, thermostablepolymerases such as ThermoSequenase™ (Amersham) or Taquenase™(ScienTech, St Louis, Mo.) are used.

The nucleotides used in the methods should be compatible with theselected polymerase. Procedures for selecting suitable nucleotide andpolymerase combinations can be adapted from Ruth et al. (1981) MolecularPharmacology 20:415-422; Kutateladze, T., et al. (1984) Nuc. Acids Res.,12:1671-1686; Chidgeavadze, Z., et al. (1985) FEBS Letters, 183:275-278.

The polymerase can be stored in a separate reservoir in the apparatusand flowed into the synthesis channels prior to each extension reactioncycle. The enzyme can also be stored together with the other reactionagents (e.g., the nucleotide triphosphates). Alternatively, thepolymerase can be immobilized onto the surface of the synthesis channelalong with the polynucleotide template.

4. Removal of Blocking Group and Labels

By repeating the incorporation and label detection steps untilincorporation is detected, the nucleotide on the template adjacent the3′ end of the primer can be identified. Once this has been achieved, thelabel should be removed before repeating the process to discover theidentity of the next nucleotide. Removal of the label can be effected byremoval of the labeled nucleotide using a 3′-5′ exonuclease andsubsequent replacement with an unlabeled nucleotide. Alternatively, thelabeling group can be removed from the nucleotide. In a furtheralternative, where the label is a fluorescent label, it is possible toneutralize the label by bleaching it with radiation. Photobleaching canbe performed according to methods, e.g., as described in Jacobson etal., “International Workshop on the Application of FluorescencePhotobleaching Techniques to Problems in Cell Biology”, FederationProceedings, 42:72-79, 1973; Okabe et al., J Cell Biol 120:1177-86,1993; and Close et al., Radiat Res 53:349-57, 1973.

If chain terminators or 3′ blocking groups have been used, these shouldbe removed before the next cycle can take place. 3′ blocking groups canbe removed by chemical or enzymatic cleavage of the blocking group fromthe nucleotide. For example, chain terminators are removed with a 3′-5′exonuclease, e.g., exonuclease III. Once the label andterminators/locking groups have been removed, the cycle is repeated todiscover the identity of the next nucleotide.

Removal of the blocking groups can be unnecessary if the labels areremovable. In this approach, the chains incorporating the blockednucleotides are permanently terminated and no longer participate in theelongation processes. So long as these blocked nucleotides are alsoremoved from the labeling process, a small percentage of permanent lossin each cycle can also be tolerated.

In some methods, other than labeled nucleotides, nucleotideincorporation is monitored by detection of pyrophosphate release (see,e.g., WO98/13523, WO98/28440, and Ronaghi et al., Science 281:363,1998). For example, a pyrophosphate-detection enzyme cascade is includedin the reaction mixture in order to produce a chemoluminescent signal.Also, instead of deoxynucleotides or dideoxynucleotides, nucleotideanalogues are used which are capable of acting as substrates for thepolymerase but incapable of acting as substrates for thepyrophosphate-detection enzyme. Pyrophosphate is released uponincorporation of a deoxynucleotide or dideoxynucleotide, which can bedetected enzymatically. This method employs no wash steps, insteadrelying on continual addition of reagents.

D. Detection of Incorporated Signals and Scanning System

1. Optical Detection

Methods for visualizing single molecules of DNA labeled with anintercalating dye include, e.g., fluorescence microscopy as described inHouseal et al., Biophysical Journal 56: 507, 1989. While usually signalsfrom a plurality of molecules are to be detected with the sequencingmethods of the present invention, fluorescence from single fluorescentdye molecules can also be detected. For example, a number of methods areavailable for this purpose (see, e.g., Nie et al., Science 266: 1013,1994; Funatsu et al., Nature 374: 555, 1995; Mertz et al., OpticsLetters 20: 2532, 1995; and Unger et al., Biotechniques 27:1008, 1999).Even the fluorescent spectrum and lifetime of a single molecule beforeit photobleaches can be measured (Macklin et al., Science 272: 255,1996). Standard detectors such as a photomultiplier tube or avalanchephotodiode can be used. Full field imaging with a two stage imageintensified CCD camera can also used (Funatsu et al., supra).

The detection system for the signal or label can also depend upon thelabel used, which can be defined by the chemistry available. For opticalsignals, a combination of an optical fiber or charged couple device(CCD) can be used in the detection step. In those circumstances wherethe matrix is itself transparent to the radiation used, it is possibleto have an incident light beam pass through the substrate with thedetector located opposite the substrate from the polynucleotides. Forelectromagnetic labels, various forms of spectroscopy systems can beused. Various physical orientations for the detection system areavailable and discussion of important design parameters is provided,e.g., in Jovin, Adv. in Biochem. Bioplyms.

Incorporated signals can be detected by scanning the synthesis channels.The synthesis channels can be scanned simultaneously or serially,depending on the scanning method used. The signals can be scanned usinga CCD camera (TE/CCD512SF, Princeton Instruments, Trenton, N.J.) withsuitable optics (Ploem, J. S., in Fluorescent and Luminescent Probes forBiological Activity, Mason, T. W., Ed., Academic Press, London, pp.1-11, 1993), such as described in Yershov et al. (Proc. Natl. Acad. Sci.93:4913, 1996), or can be imaged by TV monitoring (Khrapko et al., DNASequencing 1:375, 1991). For radioactive signals (e.g., ³²P), aphosphorimager device can be used.(Johnston et al., Johnston, R. F., etal., Electrophoresis 11:355, 1990; and Drmanac et al., Drmanac, R., etal., Electrophoresis 13:566, 1992). These methods are particularlyuseful to achieve simultaneous scanning of multiple probe-regions.

For fluorescence labeling, the synthesis channels can be seriallyscanned one by one or row by row using a fluorescence microscopeapparatus, such as described in U.S. Pat. Nos. 6,094,274, 5,902,723,5,424,186, and 5,091,652. In some methods, standard low-light levelcameras, such as a SIT and image intensified CCD camera, are employed(see, Funatsu et al., Nature 374, 555, 1995). An ICCD can be preferableto a cooled CCD camera because of its better time resolution. Thesedevices are commercially available (e.g., from Hammamatsu).

Alternatively, only the intensifier unit from Hammamatsu or DEP are usedand incorporated into other less expensive or home built cameras. Ifnecessary, the intensifier can be cooled. For example, CCD camera can bepurchased from Phillips, who offer a low priced, low noise (40 electronreadout noise per pixel) model. A home built camera allows greaterflexibility in the choice of components and a higher performance device.The advantage of using a camera instead of an avalanche photodiode isthat one can image the whole field of view. This extra spatialinformation allows the development of new noise reduction techniques.For example, one can use the fact that signals are expected from certainspatial locations (i.e. where the polynucleotide template is attached)in order to reject noise. In some applications, fluorescent excitationis exerted with a Q-switched frequency doubled Nd YAG laser, which has aKHz repetition rate, allowing many samples to be taken per second. Forexample, a wavelength of 532 nm is ideal for the excitation ofrhodamine. It is a standard device that has been used in the singlemolecule detection scheme (Smith et al., Science 253:1122, 1992). Apulsed laser allows time resolved experiments, which are useful forrejecting extraneous noise. In some methods, excitation can be performedwith a mercury lamp and signals from the incorporated nucleotides can bedetected with an inexpensive CCD camera (see, e.g., Unger et al.,Biotechniques 27:1008, 1999.

The scanning system should be able to reproducibly scan the synthesischannels in the apparatuses. Where appropriate, e.g., for a twodimensional substrate where the synthesis channels are localized topositions thereon, the scanning system should positionally define thesynthesis channels attached thereon to a reproducible coordinate system.It is important that the positional identification of synthesis channelsbe repeatable in successive scan steps.

Various scanning systems can be employed in the apparatuses of thepresent invention. For example, electrooptical scanning devicesdescribed in, e.g., U.S. Pat. No. 5,143,854, are suitable for use withthe apparatuses of the present invention. The system could exhibit manyof the features of photographic scanners, digitizers or even compactdisk reading devices. For example, a model no. PM500-A1 x-y translationtable manufactured by Newport Corporation can be attached to a detectorunit. The x-y translation table is connected to and controlled by anappropriately programmed digital computer such as an IBM PC/AT or ATcompatible computer. The detection system can be a model no. R943-02photomultiplier tube manufactured by Hamamatsu, attached to apreamplifier, e.g., a model no. SR440 manufactured by Stanford ResearchSystems, and to a photon counter, e.g., an SR430 manufactured byStanford Research System, or a multichannel detection device. Although adigital signal can usually be preferred, there can be circumstanceswhere analog signals would be advantageous.

The stability and reproducibility of the positional localization inscanning determine, to a large extent, the resolution for separatingclosely positioned polynucleotide clusters on a 2 dimensional substrate.Since the successive monitoring at a given position depends upon theability to map the results of a reaction cycle to its effect on apositionally mapped cluster of polynucleotides, high resolution scanningis preferred. As the resolution increases, the upper limit to the numberof possible polynucleotides which can be sequenced on a single matrixalso increases. Crude scanning systems can resolve only on the order of1000 μm, refined scanning systems can resolve on the order of 100 μm,more refined systems can resolve on the order of about 10 μm, and withoptical magnification systems a resolution on the order of 1.0 μm isavailable. The limitations on the resolution can be diffraction limitedand advantages can arise from using shorter wavelength radiation forfluorescent scanning steps. However, with increased resolution, the timerequired to fully scan a matrix can increased and a compromise betweenspeed and resolution can be selected. Parallel detection devices whichprovide high resolution with shorter scan times are applicable wheremultiple detectors are moved in parallel.

In some applications, resolution often is not so important andsensitivity is emphasized. However, the reliability of a signal can bepre-selected by counting photons and continuing to count for a longerperiod at positions where intensity of signal is lower. Although thisdecreases scan speed, it can increase reliability of the signaldetermination. Various signal detection and processing algorithms can beincorporated into the detection system. In some methods, thedistribution of signal intensities of pixels across the region of signalare evaluated to determine whether the distribution of intensitiescorresponds to a time positive signal.

2. Non-optical Detection

Other than fluorescently labeled nucleotides and optical detectiondevices, other methods of detecting nucleotide incorporation are alsocontemplated in the present invention, including the use of massspectrometry to analyze the reaction products, the use of radiolabelednucleotides, and detection of reaction products with “wired enzymes”.

In some methods, mass spectrometry is employed to detect nucleotideincorporation in the primer extension reaction. A primer extensionreaction consumes a nucleotide triphosphate, adds a single base to theprimer/template duplex, and produces pyrophosphate as a by-product. Massspectrometry can be used to detect pyrophosphate in the wash streamafter a nucleotide has been incubated with the template and polymerase.The absence of pyrophosphate indicates that the nucleotide was notincorporated, whereas the presence of pyrophosphate indicatesincorporation. Detection based on pyrophosphate release have beendescribed, e.g., in WO98/13523, WO98/28440, and Ronaghi et al., Science281:363, 1998.

In some methods, radiolabeled nucleotides are used. Nucleotides can beradiolabeled either in the sugar, the base, or the triphosphate group.To detect radioactivity, small radioactivity sensor can be incorporatedin the substrate on which the microfluidic chip is mounted. A CCD pixel,for instance, serves as a good detector for some radioactive decayprocesses. Radiolabeling of the sugar or base produces an additivesignal: each incorporation increases the amount of radiolabel in theprimer-template duplex. If the nucleotide is labeled in the portion thatis released as pyrophosphate (e.g. dNTP with β- or γ-³²P), theradioactive pyrophosphate can be detected in the wash stream. Thisradioactivity level is not additive, but rather binary for eachattempted nucleotide addition, so subsequent addition poses no readlength limit. Due to the small reagent consumption and contained natureof microfluidics, the total radioactivity used in such a system isrelatively minimal, and containment is relatively simple.

In some methods, non-optical detection of pyrophosphate release makesuse of “wired redox enzymes” as described, e.g., in Heller et al.,Analytical Chemistry 66:2451-2457, 1994; and Ohara et al., AnalyticalChemistry 65:3512-3517, 1993. Briefly, enzymes are covalently linked toa hydrogel matrix containing redox active groups capable of transportingcharge. The analyte to be detected is either acted on directly by aredox enzyme (either releasing or consuming electrons) or consumed as areagent in an enzymatic cascade that produces a substrate that isreduced or oxidized by a redox enzyme. The production or consumption ofelectrons is detected at a metal electrode in contact with the hydrogel.For the detection of pyrophosphate, an enzymatic cascade usingpyrophosphatase, maltose phosphorylase, and glucose oxidase can beemployed. Pyrophosphatase converts pyrophosphate into phosphate; maltosephosphorylase converts maltose (in the presence of phosphate) to glucose1-phosphate and glucose. Then, glucose oxidase converts the glucose togluconolactone and H2O2; this final reaction is the redox step whichgives rise to a detectable current at the electrode. Glucose sensorsbased on this principle are well known in the art, and enzymaticcascades as described here have been demonstrated previously. Otherenzymatic cascades besides the specific example given here are alsocontemplated the present invention. This type of detection scheme allowsdirect electrical readout of nucleotide incorporation at each reactionchamber, allowing easy parallelization.

E. Fluorescent Photobleaching Sequencing

In some methods, polynucleotide sequences are analyzed with afluorescent photobleaching method. In this methods, fluorescentlylabeled nucleotides are used in the primer extension. Signals from theincorporated nucleotides are removed by photobleaching before nextextension cycle starts.

The polynucleotide templates can be prepared as described above (e.g.,cloning in single-stranded M13 plasmid). Biotinylated templates areattached to surface of the synthesis channel that has been pretreatedwith the PEM technique as discussed above. After the primed, singlestranded DNA is immobilized to the synthesis channel in the flow cell. Apolymerase and one nucleotide triphosphate, e.g. dATP, are flowed intothe flow cell. A high fidelity polymerase with no exonucleaseproofreading ability is preferred. In some methods, only a fraction(e.g., less than 10%, 5%, 1%, 0.1%, 0.01%, or 0.001%) of each type ofthe nucleotide triphosphates is fluorescently labeled (e.g.,rhodamine-labeled nucleotide triphosphates from NEN DuPont). Forexample, if the first base of DNA sequence following the primer is T,then the polymerase incorporates the dATP's and some fraction of the DNAmolecules become fluorescently labeled. If the first base is anythingelse, no fluorescent molecules become incorporated. The reagents arethen flowed out of the flow cell, and the fluorescence of the DNA ismeasured. If no fluorescence is detected, the procedure is repeated withone of the other nucleotide triphosphates. If fluorescence is detected,the identity of the first base in the sequence has been determined. Thefluorescence signal is photobleached and extinguished before theprocedure is then repeated for the next base in the template sequence.

The fluorescence can be excited with, e.g., a Q-switched frequencydoubled Nd YAG laser (Smith et al., Science 253: 1122, 1992). This is astandard device used in the single molecule detection scheme thatmeasures the fluorescent spectrum and lifetime of a single moleculebefore it photobleached. It has a kHz repetition rate, allowing manysamples to be taken per second. The wavelength can be. e.g., 532 nm thatis ideal for the excitation of rhodamine. A pulsed laser allows timeresolved experiments and is useful for rejecting extraneous noise.

Detection of the incorporated label can be performed with a standardlow-light level cameras, such as a SIT or a image intensified CCD camera(Funatsu et al, supra). An Intensified CCD (ICCD) camera is preferableto a cooled CCD camera because of its better time resolution. Thesedevices are available from, e.g., Hammamatsu. However, because thesecameras are extremely expensive, a detection device can be made bybuilding just the intensifier unit from Hammamatsu into a CCD camera.Optionally, the intensifier can be cooled. The CCD camera is availablefrom Phillips, e.g., a low priced, low noise model (40 electron readoutnoise per pixel). A customarily built camera allows greater flexibilityin the choice of components and a higher performance device. Theadvantage of using a camera instead of an avalanche photodiode is thatthe whole field of view can be imaged. This extra spatial informationallows the development of new noise reduction techniques. For example,the fact that signals are expected from certain spatial locations (i.e.where the DNA is attached) can be used to reject noise.

F. Other Considerations

A combination of factors affect the read length and throughput of thesequencing analysis according to the present invention. First, all ofthe unincorporated labeled nucleotides should be removed from thesynthesis channel or reaction chamber after each cycle. Since onlyrelatively small number of incorporated dye molecules are to bedetected, the reagent exchange should be leave substantially fewerunincorporated labeled nucleotides than the number of nucleotides to bedetected. Second, the rate of reagent exchange is limited by fluidmechanic considerations. Turbulent flow should be avoided in order topreserve effective reagent exchange, and the fluid flow shear forcesshould be small enough in order to not break the DNA or dislocate theenzyme. Third, the kinetics of nucleotide incorporation and enzyme-DNAcomplex formation should be considered.

The present invention teaches how to determine acceptable flow rate offluids in the apparatuses. According to the invention, flow rate in theapparatuses with microfabricated flow channels having a depth of 100 μmis typically 0.1-1 cm/sec. For microfabricated flow channels with adepth of 10 μm, the flow rate is usually in the range of 1-10 cm/sec.Fluid flow in the apparatuses remains laminar as long as the Reynoldsnumber R≈ρυι/η<<1, where ρ is the density of the fluid, υ is thevelocity, ι is the dimension of the chamber, and η is the viscosity(see, e.g., Landau et al., Fluid Mechanics, Pergamon Press, New York,1989). The limiting velocity is in the order of 1 cm/sec for a 100 μmchannel depth. For microchannels with a depth of 10 μm, the limit is 10cm/sec.

The ultimate limit on the rate at which fluid can be exchanged isdetermined by the effect of drag and shear flows on the polynucleotidetemplate and the polymerase. The velocity profile of constrained flow isparabolic (v(τ)−v_(ave)(1−(τ/R)²)), causing a shear force. Singlemolecule experiments with double stranded DNA have shown that one canapply forces of up to F≈50 pN without breaking or causing irreversibledamage to DNA (see, e.g., Smith et al., Science 271: 795, 1996; andCluzel et al., Science 271: 792, 1996), and a similar order of magnitudeis expected for single stranded DNA. The drag coefficient of DNA α=6πR₅can be estimated from the radius of gyration R₅=0.3 μm. Then the maximumfluid velocity allowed is determined by solving the equation:

 v _(max)(R−R _(g))=F/α

The maximum average velocity before shearing of DNA becomes a problem is140 cm/sec.

Another consideration is to prevent the polymerase from falling off thetemplate or becoming damaged. With RNA polymerase, it has been shownthat the stalling force for RNA polymerase, at which it might receiveirreversible damage, is 14 pN (Yin et al., Science 270:1653, 1995).Since one the drag coefficient of a DNA polymerase can be estimated fromits size, a similar calculation as for the DNA shear leads to a maximumvelocity of 500 cm/sec.

The time to remove all of the free nucleotides can be calculated byincluding the effects of diffusion into hydrodynamic calculation of thefluid flow. There are a great variety of products available, includingelectronic switching valves with very small dead volumes. For example, asix port valve from Upchurch with electric motor from Thar Designs has adead volume of 2 μl and switching time of 166 msec. Combined with0.0025″ I.D. tubing and the estimated 1 μl capacity of themicrofabricated flow cell, 4 μl of material should be exchanged for eachstep in the process. A syringe or peristaltic pump can give very highflow rates, the limiting factor is low Reynolds number. The inverse rateconstant to get rid of all of the nucleotides is

τ=(LR/v _(ave))^(2/3)(D)^(−1/3)

where L is the linear dimension of the device and D is the diffusionconstant of the nucleotides. Plugging in approximate numbers gives atime of τ=15 sec. To reduce the nucleotide concentration from in theorder of millimolar to 1 labeled nucleotide per detection region, whichis a reduction of approximately 10⁻⁷. The amount of time to completelyflush the device is ln(10⁻⁷)τ=4 minutes.

For apparatuses with microfabricated flow channel depth of 10 μm andmicrofabricated valves incorporated on chip, the dead volume is reducedand throughput increased. The valves can provide an essentially zerodead volume and 10 msec switching time. This and the reduced dimensionsof the device leads to a drastic increase of throughput: the time toflush the reagents (e.g., nucleotides) from the system is reduced to 0.8sec. The overall throughput is approximately 1 base per second. Table 1summarizes the various factors affecting throughput of apparatuses withmicrofabricated flow channels having a depth of 100 μm or 10 μm.

TABLE I. Parameters Affecting Throughput of the Sequencing Apparatuses

I II Channel depth (μm) 100  10 Dead Volume (μl) 4  10⁻³ Turbulence vel.(cm/sec) 1  10 DNA Shear (cm/sec) 140  14 Polymerase stall (cm/sec) 1000100 Reagent exchange (sec) 240  0.8 Note that in apparatuses I, thelimiting factor is the fluid velocity that causes turbulent flow. Inapparatuses II, shear forces on the DNA also becoming limiting. Thereagent exchange time is expected to improve by a factor of 100 inapparatuses II.

The DNA polymerases can fall off of the DNA. If enzyme is replenished,it takes time for the enzyme to find and bind to a free DNA site. Thiscould affect throughput of the apparatuses. The attrition rate of thepolymerase can be determined according to methods described in the art.For example, using the kinetics of the T4 DNA polymerase as nominalvalues (Taylor et al., J. Phys. D. Appl. Phys. 24:1443, 1991), anon-rate of 11 μM⁻¹ sec⁻¹ was obtained. Hence a 1 μM concentration ofenzyme gives an on rate of 11 sec⁻¹, and after 1 second, 99.3% of theDNA have polymerase bound. In the absence of nucleotides (for example,during fluorescence measurement) the polymerase falls off of the DNAwith a time constant of 0.2 sec⁻¹ (Yin et al., Science 270:1653, 1995).In other words, after 5 seconds without nucleotides, this can become asource of attrition. It can be compensated for by the addition of freshpolymerase with every sequencing cycle of the device.

For the high throughput device (e.g., apparatus II in Table I), thereagent exchange is fast enough that polymerase falling off has nosignificant effect on the throughput. Also, the rate of incorporation ofnucleotides by the polymerase is typically about 300 bases per second.This is not a rate limiting factor for the device throughput.

Read length of the sequencing analysis can be affected by variousfactors. However, photobleaching is unlikely to cause any chemicalchanges to the polynucleotide template that prevent the attachment ofthe next base. During the photobleaching, the dye molecule is held offfrom the DNA on a linker arm, and it gives off so few photons that theinteraction cross section is negligible. Any attrition of the labelednucleotides also does not present any significant problem. Thestatistics of the photobleaching scheme are robust enough to allowsequencing to continue in spite of any attrition of the labelednucleotides. For example, if 0.1% of the bases are labeled, then after3000 bases the attrition is 95% if incorporation of a labeled nucleotideterminates strand extension completely. In other word, if one startswith 1 molecules, then on the first base one expects to get afluorescent signal from 100 dye molecules. By the 3000th base, thesignal is reduced to only 5 dye molecules. This is still detectable,since the lower limit of detection is one dye molecule.

It should also be noted that the attrition are discussed above is anextreme scenario because there is little reason to expect totalattrition for each incorporated base. Attrition is more likely to occurwhen the polymerase incorporates two successive labeled nucleotides. If1% of the bases are labeled, the chance of incorporating two labelednucleotides next to each other is 1%²=0.01%. Then the attrition rateafter 3000 bases is 25%. In other words, the signal only decreases by25% by the 3000th base. Thus, attrition does not cause a problem in thissequencing scheme.

Another factor that can affect read length is misincorporation. If theDNA polymerase is starved for the proper nucleotide, it can incorporatethe wrong nucleotide. Misincorporation efficiencies have been measuredto be three to five orders of magnitude below the efficiency for propernucleotide incorporation (Echols et al., Ann. Rev. Biochem 60:477,1991). Misincorporation can be minimized by only exposing the DNApolymerase-DNA complexes to nucleotides for as much time as is needed toincorporate the proper nucleotide. For a high fidelity DNA polymerase,misincorporation happens with a frequency of about 10⁻⁴. If dephasingdue to misincorporation is treated as total attrition, the attrition isonly 25% after 3 kb, i.e, the signal is reduced to 75% of its original.Thus, misincorporation does not hinder a 3 kb or perhaps longer readlength.

Many modifications and variations of this invention can be made withoutdeparting from its spirit and scope. The specific embodiments describedherein are for illustration only and are not intended to limit theinvention in any way.

All publications, figures, patents and patent applications cited hereinare hereby expressly incorporated by reference for all purposes to thesame extent as if each was so individually denoted.

What is claimed is:
 1. A method of analyzing a target polynucleotidecomprising: (a) pretreating the surface of a substrate with apolyelectrolyte multilayer (PEM) to create surface chemistry thatfacilitates polynucleotide attachment and sequence analysis; (b)providing a primed target polynucleotide attached to a surface of asubstrate; (c) providing a labeled first nucleotides to the attachedtarget polynucleotide under conditions whereby the labeled firstnucleotide attaches to the primer, if a complementary nucleotide ispresent to serve as template in the target polynucleotide; (d)determining presence or absence of a signal, the presence of a signalindicating that the labeled first nucleotide was incorporated into theprimer, and hence the identity of the complementary base that served asa template in the target polynucleotide; (e) repeating steps (c)-(d)with a labeled further nucleotide, the same or different from the firstlabeled nucleotide, whereby the labeled further nucleotide attaches tothe primer or a nucleotide previously incorporated into the primer; and(f) repeating step (e) until identities of the bases in a portion or allof the target polynucleotide are determined.